Variant report

Variant	rs1249724
Chromosome Location	chr9:117112633-117112634
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:117110279-117113384	GM12878	blood:	n/a	n/a
2	POLR2A	chr9:117112336-117112672	GM12891	blood:	n/a	n/a
3	POLR2A	chr9:117110376-117112652	GM12892	blood:	n/a	n/a
4	POLR2A	chr9:117109963-117113575	GM12878	blood:	n/a	n/a
5	POLR2A	chr9:117109739-117115529	K562	blood:	n/a	n/a
6	POLR2A	chr9:117110013-117112776	GM12892	blood:	n/a	n/a
7	POLR2A	chr9:117110064-117112683	GM12892	blood:	n/a	n/a
8	POLR2A	chr9:117110194-117113843	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:117111406..117113216-chr9:117113405..117115243,2	K562	blood:
2	chr9:117112335..117114082-chr9:117126722..117128876,2	K562	blood:
3	chr9:117106171..117108115-chr9:117111473..117114082,3	K562	blood:

Variant related genes	Relation type
AKNA	TF binding region

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10982172	0.81[ASN][1000 genomes]
rs10982174	0.81[ASN][1000 genomes]
rs1249723	0.81[ASN][1000 genomes]
rs1265891	0.81[ASN][1000 genomes]
rs1687393	0.81[ASN][1000 genomes]
rs1687394	0.81[ASN][1000 genomes]
rs1687397	1.00[CHB][hapmap]
rs1687420	1.00[EUR][1000 genomes]
rs16928312	1.00[EUR][1000 genomes]
rs16928348	1.00[EUR][1000 genomes]
rs16928495	1.00[EUR][1000 genomes]
rs1766069	1.00[CHB][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2787345	0.81[ASN][1000 genomes]
rs2787346	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28668428	1.00[EUR][1000 genomes]
rs57967306	1.00[EUR][1000 genomes]
rs58774465	1.00[EUR][1000 genomes]
rs58957650	1.00[EUR][1000 genomes]
rs59274247	1.00[EUR][1000 genomes]
rs60701901	1.00[EUR][1000 genomes]
rs60740853	1.00[EUR][1000 genomes]
rs61757558	1.00[EUR][1000 genomes]
rs61757559	1.00[EUR][1000 genomes]
rs7036274	1.00[EUR][1000 genomes]
rs73656046	1.00[EUR][1000 genomes]
rs7862731	1.00[EUR][1000 genomes]
rs7870904	1.00[EUR][1000 genomes]
rs7871080	1.00[EUR][1000 genomes]
rs902486	0.81[ASN][1000 genomes]
rs902488	0.81[ASN][1000 genomes]
rs902489	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs902491	0.81[ASN][1000 genomes]
rs902492	0.81[ASN][1000 genomes]
rs902493	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:35 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430093	chr9:116330446-117325446	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
2	esv2422396	chr9:116792944-117354862	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	155 gene(s)	inside rSNPs	diseases
3	esv2422492	chr9:116811294-117366643	Genic enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	155 gene(s)	inside rSNPs	diseases
4	nsv466533	chr9:116930100-117248479	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	128 gene(s)	inside rSNPs	diseases
5	nsv615233	chr9:116930100-117248479	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	128 gene(s)	inside rSNPs	diseases
6	nsv1051544	chr9:116944940-117443031	ZNF genes & repeats Genic enhancers Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
7	nsv540203	chr9:116944940-117443031	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
8	nsv1048093	chr9:116945025-117456210	Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
9	nsv1050991	chr9:116953739-117442999	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
10	nsv1046311	chr9:116953739-117447142	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
11	nsv1052877	chr9:116953739-117456210	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
12	nsv1039681	chr9:116953739-117457158	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
13	nsv1051987	chr9:116955841-117453668	Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
14	nsv1044374	chr9:116955841-117460150	Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
15	nsv466534	chr9:116956268-117455810	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
16	nsv615234	chr9:116956268-117455810	Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
17	nsv1048817	chr9:116957958-117456210	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
18	nsv615235	chr9:116958144-117367061	ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
19	nsv615236	chr9:116958144-117455810	Strong transcription Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
20	nsv466535	chr9:116958144-117456175	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
21	nsv615237	chr9:116958144-117456175	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
22	nsv615238	chr9:116958144-117458475	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
23	nsv430094	chr9:116958446-117456446	Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
24	nsv1053756	chr9:116975934-117443031	Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
25	nsv540204	chr9:116975934-117443031	Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
26	nsv1047704	chr9:116978041-117399362	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
27	nsv540205	chr9:116978041-117399362	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
28	nsv530950	chr9:117009156-117399361	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
29	nsv916139	chr9:117009169-117399454	Weak transcription Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
30	nsv1047822	chr9:117010663-117211517	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
31	nsv893757	chr9:117021374-117120680	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
32	nsv530951	chr9:117032675-117439804	Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
33	nsv893759	chr9:117066823-117120680	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
34	nsv1050256	chr9:117106276-117247033	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
35	nsv540206	chr9:117106276-117247033	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117096800-117113800	Strong transcription	Gastric	stomach
2	chr9:117096800-117114200	Strong transcription	Fetal Intestine Small	intestine
3	chr9:117096800-117115000	Strong transcription	Fetal Muscle Trunk	muscle
4	chr9:117096800-117126000	Strong transcription	Thymus	Thymus
5	chr9:117096800-117127000	Strong transcription	Rectal Mucosa Donor 31	rectum
6	chr9:117097000-117113400	Strong transcription	Liver	Liver
7	chr9:117097400-117114600	Strong transcription	Fetal Intestine Large	intestine
8	chr9:117097600-117115000	Strong transcription	Fetal Muscle Leg	muscle
9	chr9:117098600-117113200	Strong transcription	Pancreas	Pancrea
10	chr9:117103400-117125600	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr9:117103600-117125400	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr9:117104000-117113600	Strong transcription	Small Intestine	intestine
13	chr9:117104000-117125800	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr9:117106200-117115400	Strong transcription	Fetal Stomach	stomach
15	chr9:117106600-117131400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr9:117107000-117143600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr9:117107600-117113800	Strong transcription	Skeletal Muscle Male	skeletal muscle
18	chr9:117110000-117115800	Genic enhancers	Primary T cells fromperipheralblood	blood
19	chr9:117110400-117113000	Genic enhancers	Fetal Thymus	thymus
20	chr9:117110400-117114400	Genic enhancers	Primary B cells from peripheral blood	blood
21	chr9:117110400-117115000	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr9:117110400-117116800	Genic enhancers	Primary T cells from cord blood	blood
23	chr9:117110600-117112800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr9:117110600-117113000	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr9:117110600-117113000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr9:117110600-117114400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
27	chr9:117110600-117115000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr9:117110600-117116000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
29	chr9:117110600-117116800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
30	chr9:117110800-117113200	Genic enhancers	Dnd41	blood
31	chr9:117110800-117113400	Genic enhancers	Primary B cells from cord blood	blood
32	chr9:117110800-117113600	Genic enhancers	GM12878-XiMat	blood
33	chr9:117110800-117113800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr9:117110800-117114400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr9:117110800-117114400	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr9:117110800-117116000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr9:117111000-117116200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr9:117111000-117116200	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr9:117111200-117115200	Strong transcription	Fetal Lung	lung
40	chr9:117111200-117126000	Strong transcription	Lung	lung
41	chr9:117111400-117113600	Strong transcription	Left Ventricle	heart
42	chr9:117111600-117112800	Strong transcription	Stomach Mucosa	stomach
43	chr9:117111800-117113000	Strong transcription	Brain Cingulate Gyrus	brain
44	chr9:117111800-117113200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr9:117111800-117113200	Strong transcription	Aorta	Aorta
46	chr9:117111800-117113200	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr9:117111800-117113800	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr9:117111800-117113800	Strong transcription	Colonic Mucosa	Colon
49	chr9:117111800-117128200	Strong transcription	Brain Substantia Nigra	brain
50	chr9:117112000-117113200	Strong transcription	Fetal Kidney	kidney

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