Variant report

Variant	rs41306498
Chromosome Location	chr9:117139280-117139281
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	chr9:117139193-117139663	GM12878	blood:	n/a	n/a
2	POLR2A	chr9:117138580-117142231	K562	blood:	n/a	n/a
3	POLR2A	chr9:117138925-117139427	GM12878	blood:	n/a	n/a
4	POLR2A	chr9:117138708-117142020	GM12891	blood:	n/a	n/a
5	POLR2A	chr9:117139275-117139284	K562	blood:	n/a	n/a
6	POLR2A	chr9:117138930-117139675	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:117136553..117139395-chr9:117157861..117162089,3	K562	blood:

Variant related genes	Relation type
AKNA	TF binding region
ENSG00000235119	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12001020	0.86[AFR][1000 genomes]
rs12002829	0.86[AFR][1000 genomes]
rs2636904	0.96[EUR][1000 genomes]
rs2763184	0.96[EUR][1000 genomes]
rs2763185	0.96[EUR][1000 genomes]
rs55861916	0.86[AFR][1000 genomes]
rs56698173	0.86[AFR][1000 genomes]
rs58493366	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59506038	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59608349	0.86[AFR][1000 genomes]
rs73656092	0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:34 , 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	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
32	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
33	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
34	nsv831693	chr9:117116450-117281895	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117107000-117143600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
2	chr9:117117800-117145200	Strong transcription	Fetal Intestine Small	intestine
3	chr9:117124000-117146200	Weak transcription	Stomach Mucosa	stomach
4	chr9:117128800-117145000	Weak transcription	HSMMtube	muscle
5	chr9:117129200-117141200	Weak transcription	HSMM	muscle
6	chr9:117129400-117142400	Weak transcription	NH-A	brain
7	chr9:117129800-117143600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr9:117129800-117147400	Weak transcription	Hela-S3	cervix
9	chr9:117130600-117141000	Weak transcription	HepG2	liver
10	chr9:117131000-117144400	Weak transcription	Small Intestine	intestine
11	chr9:117131200-117141000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr9:117132200-117139400	Weak transcription	Fetal Kidney	kidney
13	chr9:117132800-117143600	Strong transcription	Fetal Intestine Large	intestine
14	chr9:117133600-117144000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr9:117133600-117145600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr9:117134200-117140200	Strong transcription	Sigmoid Colon	Sigmoid Colon
17	chr9:117134400-117144400	Strong transcription	Rectal Smooth Muscle	rectum
18	chr9:117134600-117143400	Strong transcription	Liver	Liver
19	chr9:117135000-117142600	Strong transcription	Stomach Smooth Muscle	stomach
20	chr9:117135000-117144600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr9:117135200-117141000	Weak transcription	Osteobl	bone
22	chr9:117135200-117143200	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
23	chr9:117135200-117144400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr9:117135200-117144800	Genic enhancers	Primary monocytes fromperipheralblood	blood
25	chr9:117135200-117144800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr9:117135200-117145200	Genic enhancers	Primary B cells from peripheral blood	blood
27	chr9:117135200-117145200	Strong transcription	Fetal Stomach	stomach
28	chr9:117135200-117147000	Weak transcription	NHEK	skin
29	chr9:117135400-117139600	Strong transcription	Colonic Mucosa	Colon
30	chr9:117135400-117141200	Genic enhancers	Primary T cells fromperipheralblood	blood
31	chr9:117135400-117143800	Strong transcription	Brain Cingulate Gyrus	brain
32	chr9:117135400-117144200	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr9:117135400-117144200	Weak transcription	Right Atrium	heart
34	chr9:117135600-117143400	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr9:117135600-117143800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr9:117135800-117141000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr9:117135800-117142000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr9:117135800-117143400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr9:117135800-117143800	Strong transcription	Colon Smooth Muscle	Colon
40	chr9:117135800-117144600	Genic enhancers	Thymus	Thymus
41	chr9:117135800-117145000	Genic enhancers	Fetal Thymus	thymus
42	chr9:117135800-117145600	Weak transcription	HUVEC	blood vessel
43	chr9:117136000-117139800	Genic enhancers	GM12878-XiMat	blood
44	chr9:117136000-117140400	Strong transcription	Duodenum Mucosa	Duodenum
45	chr9:117136000-117141000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr9:117136000-117144400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr9:117136000-117144800	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr9:117136200-117141200	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr9:117136200-117141400	Genic enhancers	Primary neutrophils fromperipheralblood	blood
50	chr9:117136200-117142000	Strong transcription	Rectal Mucosa Donor 31	rectum

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