Variant report

Variant	rs2402866
Chromosome Location	chr7:127294107-127294108
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	WRNIP1	chr7:127293989-127295015	GM12878	blood:	n/a	n/a
2	NRF1	chr7:127291536-127294324	SK-N-SH	brain:	n/a	chr7:127292203-127292212 chr7:127292201-127292212 chr7:127292201-127292215
3	POLR2A	chr7:127294056-127295037	K562	blood:	n/a	n/a
4	POLR2A	chr7:127293720-127294792	GM12878	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:127222868..127230871-chr7:127290370..127294912,16	K562	blood:
2	chr7:127292643..127294147-chr7:127310003..127312142,2	MCF-7	breast:
3	chr7:127292385..127294984-chr7:127328196..127329892,2	K562	blood:
4	chr7:127223375..127232960-chr7:127286940..127295803,24	K562	blood:
5	chr7:127029920..127034279-chr7:127291168..127294285,4	MCF-7	breast:
6	chr7:127029926..127034103-chr7:127290516..127296284,10	K562	blood:
7	chr7:127292635..127294692-chr7:127327406..127330053,2	MCF-7	breast:
8	chr7:127028627..127034604-chr7:127290902..127294330,10	K562	blood:
9	chr7:127292301..127294616-chr7:127313829..127315529,2	MCF-7	breast:
10	chr7:127293455..127295442-chr7:127314786..127317703,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000240790	TF binding region
ENSG00000004059	Chromatin interaction
ENSG00000048405	Chromatin interaction
ENSG00000106328	Chromatin interaction
ENSG00000179562	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10251423	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10251548	0.86[EUR][1000 genomes]
rs1029927	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10954163	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11521053	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11971935	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11972774	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11976841	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11976946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11977012	0.96[ASN][1000 genomes]
rs11977915	0.94[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11980318	0.94[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12531440	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12533846	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12539728	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12540865	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13236900	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13237048	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs141450	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16885524	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17151241	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17151270	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17716738	0.94[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17718395	0.85[ASN][1000 genomes]
rs1860934	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1881084	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2014583	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2016786	0.92[EUR][1000 genomes]
rs2043982	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2119452	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2119453	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2141259	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2402867	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2402870	0.92[EUR][1000 genomes]
rs325440	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs325442	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs325444	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs325445	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs325446	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs325447	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs325451	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs327518	0.85[CHB][hapmap];0.94[CHD][hapmap];0.83[ASN][1000 genomes]
rs35121681	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35176520	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35940771	0.92[EUR][1000 genomes]
rs35971861	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3779529	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3779530	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3808092	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3808093	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3808095	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3808097	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3808105	0.96[ASN][1000 genomes]
rs3808106	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3808107	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3808112	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3824006	0.88[CHD][hapmap]
rs4728077	0.96[ASN][1000 genomes]
rs4731376	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4731378	0.92[EUR][1000 genomes]
rs55694225	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56306023	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58583807	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6467145	0.92[EUR][1000 genomes]
rs6961381	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6963455	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6968199	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6969880	0.87[EUR][1000 genomes]
rs712712	0.97[EUR][1000 genomes]
rs712716	1.00[CEU][hapmap];0.90[JPT][hapmap];0.98[EUR][1000 genomes]
rs73234861	0.96[ASN][1000 genomes]
rs73234862	0.96[ASN][1000 genomes]
rs73234880	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73234882	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73234897	0.85[ASN][1000 genomes]
rs741599	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs759843	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7785050	0.88[EUR][1000 genomes]
rs7797663	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7799882	0.92[EUR][1000 genomes]
rs917832	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs918793	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs972088	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs972089	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs972090	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831122	chr7:127143207-127357885	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv1022385	chr7:127246656-127971194	Weak transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv539120	chr7:127246656-127971194	Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1016143	chr7:127251359-127726762	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1031658	chr7:127266882-127376775	Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv831123	chr7:127289511-127510396	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2402866	HYAL4	cis	cerebellum	SCAN
rs2402866	SND1	cis	parietal	SCAN
rs2402866	GPR37	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127291000-127294200	Active TSS	H1 Cell Line	embryonic stem cell
2	chr7:127291200-127294400	Active TSS	Pancreas	Pancrea
3	chr7:127291200-127294600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr7:127291200-127294600	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr7:127291400-127294400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr7:127291400-127294800	Active TSS	NHLF	lung
7	chr7:127291600-127294800	Active TSS	Placenta	Placenta
8	chr7:127292000-127294200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr7:127292800-127294400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr7:127292800-127296200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr7:127293000-127294200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr7:127293000-127294200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
13	chr7:127293000-127294600	Flanking Active TSS	HUVEC	blood vessel
14	chr7:127293000-127295000	Flanking Active TSS	Liver	Liver
15	chr7:127293000-127296200	Enhancers	Fetal Heart	heart
16	chr7:127293000-127296400	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr7:127293000-127304000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr7:127293200-127294200	Enhancers	Brain Germinal Matrix	brain
19	chr7:127293200-127294400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr7:127293200-127294400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr7:127293200-127294400	Weak transcription	Esophagus	oesophagus
22	chr7:127293200-127294400	Enhancers	Fetal Brain Male	brain
23	chr7:127293200-127294400	Weak transcription	Gastric	stomach
24	chr7:127293200-127294400	Weak transcription	Lung	lung
25	chr7:127293200-127294400	Weak transcription	Spleen	Spleen
26	chr7:127293200-127294800	Enhancers	Fetal Kidney	kidney
27	chr7:127293200-127294800	Enhancers	Placenta Amnion	Placenta Amnion
28	chr7:127293200-127295000	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr7:127293200-127295000	Enhancers	Primary T cells fromperipheralblood	blood
30	chr7:127293200-127295000	Enhancers	Brain Substantia Nigra	brain
31	chr7:127293200-127295000	Enhancers	Fetal Lung	lung
32	chr7:127293200-127295000	Enhancers	Fetal Thymus	thymus
33	chr7:127293200-127295000	Enhancers	Rectal Smooth Muscle	rectum
34	chr7:127293200-127295200	Enhancers	Primary B cells from cord blood	blood
35	chr7:127293200-127295200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr7:127293200-127295200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
37	chr7:127293200-127295200	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr7:127293200-127295400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr7:127293200-127295400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr7:127293200-127295400	Enhancers	Thymus	Thymus
41	chr7:127293200-127295600	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr7:127293200-127295600	Enhancers	Brain Anterior Caudate	brain
43	chr7:127293200-127295600	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr7:127293200-127296000	Enhancers	Primary B cells from peripheral blood	blood
45	chr7:127293200-127296000	Enhancers	Stomach Mucosa	stomach
46	chr7:127293200-127296200	Enhancers	Small Intestine	intestine
47	chr7:127293200-127296400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
48	chr7:127293200-127296800	Enhancers	Left Ventricle	heart
49	chr7:127293200-127302200	Weak transcription	Aorta	Aorta
50	chr7:127293200-127304200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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