Variant report

Variant	rs10516523
Chromosome Location	chr4:106625263-106625264
allele	G/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	FOS	chr4:106625244-106625442	MCF10A-Er-Src	breast:	n/a	chr4:106625370-106625377 chr4:106625369-106625378 chr4:106625369-106625377
2	FOS	chr4:106625239-106625531	MCF10A-Er-Src	breast:	n/a	chr4:106625370-106625377 chr4:106625369-106625378 chr4:106625369-106625377

No.	Distal block	Cell Line	Cell type
1	chr4:106619010..106621015-chr4:106623731..106625393,2	K562	blood:
2	chr4:106622664..106627326-chr4:106627806..106630924,8	MCF-7	breast:
3	chr4:106621555..106624339-chr4:106624780..106626817,2	K562	blood:
4	chr4:106625095..106627707-chr4:106631169..106633895,2	MCF-7	breast:
5	chr4:106610718..106612290-chr4:106624783..106626810,2	MCF-7	breast:
6	chr4:106609114..106611557-chr4:106624623..106627601,2	K562	blood:
7	chr4:106623594..106626917-chr4:106627781..106630373,5	K562	blood:
8	chr4:106616699..106623307-chr4:106623731..106631342,11	K562	blood:

Variant related genes	Relation type
GSTCD	TF binding region
ENSG00000138785	Chromatin interaction
ENSG00000236699	Chromatin interaction
ENSG00000138780	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10025790	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs11722731	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11933386	0.81[EUR][1000 genomes]
rs11933466	1.00[CEU][hapmap];0.82[CHB][hapmap];0.98[TSI][hapmap]
rs11934139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11941690	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12639750	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1294667	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1294669	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1294670	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1294673	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13120110	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13138544	0.85[CHD][hapmap]
rs13147012	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13148869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17036098	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17262764	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2044536	0.82[CEU][hapmap];0.95[CHD][hapmap]
rs2080789	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2544395	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2544398	1.00[CEU][hapmap];0.82[CHB][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes]
rs2544404	0.81[EUR][1000 genomes]
rs2544405	0.81[EUR][1000 genomes]
rs2544406	0.82[CHB][hapmap]
rs2544408	0.82[CHB][hapmap]
rs2544409	0.82[CHB][hapmap]
rs2544412	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2544413	1.00[CEU][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2544425	0.82[CHB][hapmap]
rs2553432	0.81[EUR][1000 genomes]
rs2553436	0.81[EUR][1000 genomes]
rs2553438	0.80[EUR][1000 genomes]
rs2553441	0.81[EUR][1000 genomes]
rs2553445	0.82[AFR][1000 genomes]
rs2553449	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2553453	0.82[CHB][hapmap]
rs2553458	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2553462	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2553468	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28628106	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3756260	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4699196	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6533218	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6820200	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7680134	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7684442	0.85[AMR][1000 genomes]
rs7684839	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7685231	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs921113	0.82[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879699	chr4:106212562-106698892	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106587800-106629000	Weak transcription	Lung	lung
2	chr4:106600400-106628600	Weak transcription	Colonic Mucosa	Colon
3	chr4:106600600-106628400	Weak transcription	Stomach Mucosa	stomach
4	chr4:106601200-106628400	Weak transcription	Psoas Muscle	Psoas
5	chr4:106602200-106629200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:106602400-106628600	Weak transcription	Right Ventricle	heart
7	chr4:106602600-106628400	Weak transcription	Fetal Heart	heart
8	chr4:106602600-106629200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr4:106604400-106629200	Weak transcription	Esophagus	oesophagus
10	chr4:106604400-106629200	Weak transcription	Gastric	stomach
11	chr4:106606600-106628200	Weak transcription	Hela-S3	cervix
12	chr4:106607600-106626400	Weak transcription	Small Intestine	intestine
13	chr4:106610400-106628800	Weak transcription	Fetal Kidney	kidney
14	chr4:106610600-106628200	Weak transcription	Fetal Brain Male	brain
15	chr4:106610600-106628600	Weak transcription	A549	lung
16	chr4:106610800-106628600	Weak transcription	Brain Cingulate Gyrus	brain
17	chr4:106611400-106627600	Weak transcription	HepG2	liver
18	chr4:106611400-106628600	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr4:106613600-106628600	Weak transcription	Aorta	Aorta
20	chr4:106613600-106628600	Weak transcription	Ovary	ovary
21	chr4:106614600-106628400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr4:106614800-106628200	Weak transcription	Brain Angular Gyrus	brain
23	chr4:106615000-106628600	Weak transcription	Colon Smooth Muscle	Colon
24	chr4:106615400-106626000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr4:106615800-106628600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr4:106615800-106628600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr4:106616000-106628400	Weak transcription	NHLF	lung
28	chr4:106616000-106628600	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr4:106616000-106629000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr4:106616200-106628400	Weak transcription	Brain Germinal Matrix	brain
31	chr4:106616400-106628400	Weak transcription	Thymus	Thymus
32	chr4:106616400-106628600	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr4:106616800-106628600	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr4:106616800-106628600	Weak transcription	NH-A	brain
35	chr4:106617400-106627600	Weak transcription	Fetal Intestine Small	intestine
36	chr4:106617400-106628600	Weak transcription	Fetal Intestine Large	intestine
37	chr4:106617400-106628800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr4:106617400-106629000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr4:106617400-106629000	Weak transcription	Pancreas	Pancrea
40	chr4:106617600-106626200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr4:106617600-106628000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr4:106617600-106628400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr4:106617600-106628400	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr4:106618200-106626400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr4:106619200-106628600	Weak transcription	Fetal Stomach	stomach
46	chr4:106619200-106629000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr4:106619400-106628600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr4:106619400-106628600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr4:106619400-106628600	Weak transcription	Stomach Smooth Muscle	stomach
50	chr4:106619600-106626200	Weak transcription	Fetal Lung	lung

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