Variant report

Variant	rs13230660
Chromosome Location	chr7:104651058-104651059
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:31)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:31 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr7:104650846-104651523	K562	blood:	n/a	chr7:104651324-104651335
2	POLR2A	chr7:104649871-104658724	K562	blood:	n/a	n/a
3	POLR2A	chr7:104650500-104651456	GM12878	blood:	n/a	n/a
4	POLR2A	chr7:104650139-104656413	GM12878	blood:	n/a	n/a
5	POLR2A	chr7:104650956-104652134	U87	brain:	n/a	n/a
6	JUND	chr7:104650542-104656365	SK-N-SH	brain:	n/a	chr7:104654505-104654514 chr7:104653596-104653605
7	CHD1	chr7:104650715-104657296	GM12878	blood:	n/a	n/a
8	POLR2A	chr7:104649793-104655808	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr7:104650238-104656311	GM12891	blood:	n/a	n/a
10	POLR2A	chr7:104650113-104654922	HepG2	liver:	n/a	n/a
11	EBF1	chr7:104651022-104651196	GM12878	blood:	n/a	n/a
12	POLR2A	chr7:104650286-104655760	HUVEC	blood vessel:	n/a	n/a
13	HEY1	chr7:104650591-104651457	K562	blood:	n/a	n/a
14	IRF1	chr7:104650448-104656728	K562	blood:	n/a	chr7:104652192-104652212 chr7:104653598-104653607 chr7:104656077-104656087 chr7:104651485-104651498 chr7:104652632-104652642 chr7:104653674-104653687 chr7:104652628-104652642 chr7:104651982-104651994
15	POLR2A	chr7:104650679-104652083	A549	lung:	n/a	n/a
16	MXI1	chr7:104649971-104659449	SK-N-SH	brain:	n/a	n/a
17	CHD1	chr7:104650096-104658695	IMR90	lung:	n/a	n/a
18	POLR2A	chr7:104650788-104657220	GM12878	blood:	n/a	n/a
19	POLR2A	chr7:104650231-104656216	GM12878	blood:	n/a	n/a
20	POLR2A	chr7:104650339-104656433	IMR90	lung:	n/a	n/a
21	POLR2A	chr7:104650962-104652057	U87	brain:	n/a	n/a
22	POLR2A	chr7:104650579-104655923	HUVEC	blood vessel:	n/a	n/a
23	POLR2A	chr7:104650663-104651608	GM12892	blood:	n/a	n/a
24	POLR2A	chr7:104651038-104651498	H1-hESC	embryonic stem cell:	n/a	n/a
25	ZNF143	chr7:104651012-104651138	GM12878	blood:	n/a	n/a
26	POLR2A	chr7:104650440-104656270	HepG2	liver:	n/a	n/a
27	WRNIP1	chr7:104650169-104651495	GM12878	blood:	n/a	n/a
28	POLR2A	chr7:104649911-104656477	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr7:104649959-104656247	MCF10A-Er-Src	breast:	n/a	n/a
30	POLR2A	chr7:104650360-104651247	SK-N-SH	brain:	n/a	n/a
31	POLR2A	chr7:104650408-104651170	HepG2	liver:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:72476582..72478189-chr7:104650247..104653086,2	MCF-7	breast:
2	chr7:104592455..104594379-chr7:104649567..104651411,2	K562	blood:
3	chr7:104650546..104656206-chr7:104695535..104706992,23	K562	blood:
4	chr7:104561816..104567252-chr7:104650571..104656074,9	K562	blood:
5	chr7:104650837..104656019-chr7:105026206..105030997,7	K562	blood:
6	chr7:104650731..104653213-chr7:104739890..104742351,2	K562	blood:
7	chr7:104649355..104651089-chr7:105173782..105176536,2	K562	blood:
8	chr7:104649613..104651128-chr7:104876520..104878391,2	K562	blood:
9	chr7:104647926..104656528-chr7:104691112..104706949,31	K562	blood:
10	chr7:104649592..104657753-chr7:104694428..104703365,16	MCF-7	breast:
11	chr7:104649601..104653676-chr7:105029497..105032094,4	K562	blood:
12	chr7:104650505..104654814-chr7:104745765..104750461,6	K562	blood:
13	chr11:65269920..65271716-chr7:104650718..104653065,2	K562	blood:
14	chr7:104648889..104654837-chr7:104768923..104775807,9	K562	blood:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SRPK2-1	chr7:104637584-104654636	NONHSAT122594
2	lnc-SRPK2-1	chr7:104650989-104653494	NONHSAT122595
3	lnc-SRPK2-1	chr7:104650989-104654588	NONHSAT122596

No data

Variant related genes	Relation type
KMT2E	TF binding region
ENSG00000272918	Chromatin interaction
ENSG00000005483	Chromatin interaction
ENSG00000135250	Chromatin interaction
ENSG00000225329	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs1013016	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1019040	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10224526	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10231782	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10231975	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10241374	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10242713	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10244764	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10245589	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10245676	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10245796	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10249746	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10249965	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10253962	0.90[EUR][1000 genomes]
rs10260346	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10261472	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10261573	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10264273	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10268866	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10274607	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10276583	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10279486	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10279602	0.92[EUR][1000 genomes]
rs10280009	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10280752	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10808139	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10808140	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10953464	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10953466	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10953467	0.91[EUR][1000 genomes]
rs11971732	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11973516	0.86[AMR][1000 genomes]
rs11976329	0.91[EUR][1000 genomes]
rs11981399	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12171585	0.84[EUR][1000 genomes]
rs12531424	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12532062	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12532456	0.92[EUR][1000 genomes]
rs12534140	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12540007	0.91[EUR][1000 genomes]
rs12667625	0.87[EUR][1000 genomes]
rs12671368	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12705297	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12705299	0.90[EUR][1000 genomes]
rs2011258	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2058711	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2216107	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2237602	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2237604	0.88[EUR][1000 genomes]
rs2237605	0.91[EUR][1000 genomes]
rs2240453	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2240454	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2240455	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2240457	0.91[EUR][1000 genomes]
rs2285532	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299299	0.90[EUR][1000 genomes]
rs28434158	0.87[EUR][1000 genomes]
rs28489493	0.92[EUR][1000 genomes]
rs2891761	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3173872	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3213676	0.91[EUR][1000 genomes]
rs3213741	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34202980	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34558707	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35780942	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3735377	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3815256	0.80[EUR][1000 genomes]
rs4730065	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4730067	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4730068	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4730069	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs67739707	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6952534	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6972229	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs71562633	0.85[EUR][1000 genomes]
rs740297	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs740298	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs740300	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7785197	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7800233	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7805792	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7810119	0.91[EUR][1000 genomes]
rs7811349	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs875567	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs875568	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs916704	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs960437	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9641340	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9641341	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs999895	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029283	chr7:104571741-104729168	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	132 gene(s)	inside rSNPs	diseases
2	nsv888927	chr7:104614664-104781644	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
3	esv2829879	chr7:104618318-104652671	Transcr. at gene 5' and 3' Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv608068	chr7:104622402-104757483	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	132 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:104641800-104651800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:104642400-104652200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr7:104648400-104651800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:104648400-104651800	Weak transcription	Pancreas	Pancrea
5	chr7:104648600-104652000	Transcr. at gene 5' and 3'	Dnd41	blood
6	chr7:104648600-104658800	Active TSS	Ovary	ovary
7	chr7:104648800-104651600	Flanking Active TSS	Adipose Nuclei	Adipose
8	chr7:104649000-104652800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr7:104649000-104657400	Active TSS	Colonic Mucosa	Colon
10	chr7:104649200-104651800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr7:104649200-104652000	Transcr. at gene 5' and 3'	K562	blood
12	chr7:104649200-104652200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr7:104649200-104653000	Active TSS	Right Atrium	heart
14	chr7:104649200-104659000	Active TSS	Right Ventricle	heart
15	chr7:104649400-104651600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
16	chr7:104649400-104651600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
17	chr7:104649400-104651800	Weak transcription	Spleen	Spleen
18	chr7:104649400-104652000	Flanking Active TSS	Primary T cells from cord blood	blood
19	chr7:104649400-104652600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
20	chr7:104649400-104652600	Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr7:104649400-104656800	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr7:104649400-104658800	Active TSS	Aorta	Aorta
23	chr7:104649400-104659400	Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr7:104649600-104651200	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr7:104649600-104651600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr7:104649600-104653200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr7:104649600-104657000	Active TSS	Colon Smooth Muscle	Colon
28	chr7:104649600-104658600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr7:104649600-104658800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr7:104649600-104659600	Active TSS	NHLF	lung
31	chr7:104649800-104651200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr7:104649800-104651400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
33	chr7:104649800-104652000	Flanking Active TSS	Brain Cingulate Gyrus	brain
34	chr7:104649800-104654000	Active TSS	Stomach Smooth Muscle	stomach
35	chr7:104649800-104656400	Active TSS	Sigmoid Colon	Sigmoid Colon
36	chr7:104649800-104657000	Active TSS	NHEK	skin
37	chr7:104649800-104657600	Active TSS	Fetal Stomach	stomach
38	chr7:104649800-104657600	Active TSS	Rectal Mucosa Donor 29	rectum
39	chr7:104649800-104658200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr7:104649800-104658600	Active TSS	Left Ventricle	heart
41	chr7:104650000-104651200	Flanking Active TSS	Osteobl	bone
42	chr7:104650000-104651400	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
43	chr7:104650000-104657200	Active TSS	Fetal Intestine Large	intestine
44	chr7:104650000-104658000	Active TSS	Duodenum Mucosa	Duodenum
45	chr7:104650000-104658600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr7:104650000-104658600	Active TSS	Psoas Muscle	Psoas
47	chr7:104650200-104651200	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr7:104650200-104651400	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
49	chr7:104650200-104651400	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
50	chr7:104650200-104651800	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived

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