Variant report

Variant	rs9810991
Chromosome Location	chr3:48583650-48583651
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:48504638..48507562-chr3:48580974..48584844,3	MCF-7	breast:
2	chr3:48508547..48510536-chr3:48581304..48583725,2	K562	blood:
3	chr3:48575329..48579039-chr3:48581677..48584572,3	K562	blood:
4	chr3:48540004..48544821-chr3:48582947..48586944,4	MCF-7	breast:
5	chr3:48579149..48580932-chr3:48582283..48584303,2	K562	blood:
6	chr3:48575329..48578020-chr3:48582630..48584572,2	K562	blood:
7	chr3:48546575..48548202-chr3:48583310..48585559,2	K562	blood:

Variant related genes	Relation type
ENSG00000164054	Chromatin interaction
ENSG00000213689	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1003649	0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.81[TSI][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes]
rs10049154	0.82[ASN][1000 genomes]
rs10470687	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];0.88[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11706983	0.83[GIH][hapmap]
rs11708786	0.83[GIH][hapmap]
rs11719291	0.83[GIH][hapmap]
rs12107252	0.83[GIH][hapmap]
rs12107418	0.83[GIH][hapmap]
rs13060933	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13062576	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[ASN][1000 genomes]
rs13063312	0.89[CHD][hapmap];0.83[GIH][hapmap]
rs13064619	0.82[ASN][1000 genomes]
rs13070798	0.83[GIH][hapmap]
rs13091944	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[ASN][1000 genomes]
rs13094578	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[ASN][1000 genomes]
rs13100178	0.86[ASN][1000 genomes]
rs13319635	0.94[ASN][1000 genomes]
rs13319651	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[ASN][1000 genomes]
rs13324142	0.89[CHD][hapmap];0.83[GIH][hapmap]
rs13434258	0.83[GIH][hapmap]
rs17080289	0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2006871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[TSI][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2276850	0.89[CHD][hapmap];0.83[GIH][hapmap]
rs2276852	0.85[CHD][hapmap];0.83[GIH][hapmap]
rs2286652	0.83[GIH][hapmap]
rs2310996	0.89[CHD][hapmap];0.83[GIH][hapmap]
rs2854394	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2854395	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28563843	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28581474	0.86[ASN][1000 genomes]
rs28881595	0.81[ASN][1000 genomes]
rs35064573	0.83[GIH][hapmap]
rs35343040	0.80[ASN][1000 genomes]
rs35562294	0.92[ASN][1000 genomes]
rs3755819	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3821876	0.89[CHD][hapmap];0.83[GIH][hapmap]
rs3969942	0.90[CHD][hapmap];1.00[GIH][hapmap];0.86[ASN][1000 genomes]
rs4075082	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6442126	0.86[CHB][hapmap]
rs6442127	0.85[ASN][1000 genomes]
rs6765317	0.80[ASN][1000 genomes]
rs6781283	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6785845	0.82[ASN][1000 genomes]
rs6792156	0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.88[MEX][hapmap];0.82[ASN][1000 genomes]
rs6792525	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6806059	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6809981	0.82[ASN][1000 genomes]
rs740787	0.89[CHD][hapmap];0.83[GIH][hapmap]
rs7428949	0.89[CHB][hapmap];0.86[ASN][1000 genomes]
rs7434077	0.89[CHB][hapmap];0.85[CHD][hapmap];0.86[ASN][1000 genomes]
rs7434107	0.86[ASN][1000 genomes]
rs7623614	0.86[ASN][1000 genomes]
rs7631574	0.89[CHD][hapmap];0.83[GIH][hapmap]
rs7640031	0.86[ASN][1000 genomes]
rs7644771	0.86[ASN][1000 genomes]
rs9810549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9811318	0.83[GIH][hapmap]
rs9812200	0.83[GIH][hapmap]
rs9814951	0.85[GIH][hapmap]
rs9816942	0.86[ASN][1000 genomes]
rs9822677	0.82[ASN][1000 genomes]
rs9830581	0.90[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.80[ASN][1000 genomes]
rs9835827	0.82[ASN][1000 genomes]
rs9835902	1.00[CEU][hapmap];0.89[CHB][hapmap];0.80[CHD][hapmap];0.85[GIH][hapmap];0.85[ASN][1000 genomes]
rs9836462	0.84[CHD][hapmap];0.83[GIH][hapmap]
rs9837687	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9841602	0.83[GIH][hapmap]
rs9843316	0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.80[ASN][1000 genomes]
rs9848824	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9849280	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9850102	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9851743	0.86[ASN][1000 genomes]
rs9851771	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.86[ASN][1000 genomes]
rs9864729	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9869698	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9871180	1.00[CEU][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9871608	0.86[ASN][1000 genomes]
rs9875911	1.00[GIH][hapmap]
rs9878950	0.87[ASW][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.88[MEX][hapmap];0.93[MKK][hapmap];0.81[TSI][hapmap];0.86[YRI][hapmap];0.94[ASN][1000 genomes]
rs9881877	0.93[ASW][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.81[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9882549	0.83[GIH][hapmap]
rs9882962	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.80[EUR][1000 genomes];0.91[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	nsv834684	chr3:48385699-48589323	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv1008232	chr3:48517121-48702416	Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv523981	chr3:48520289-48721040	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv1004383	chr3:48543794-48649772	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS 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	28 gene(s)	inside rSNPs	diseases
5	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
6	esv3406976	chr3:48581748-48585946	Strong transcription Genic enhancers Weak transcription Enhancers	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48547600-48591600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:48556200-48586800	Strong transcription	HUES64 Cell Line	embryonic stem cell
3	chr3:48556400-48586400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:48559600-48586400	Weak transcription	Primary B cells from cord blood	blood
5	chr3:48562600-48592000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:48568800-48586000	Weak transcription	Colon Smooth Muscle	Colon
7	chr3:48570600-48591600	Weak transcription	Fetal Brain Male	brain
8	chr3:48572200-48583800	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr3:48573400-48584400	Weak transcription	Fetal Kidney	kidney
10	chr3:48573600-48589600	Weak transcription	Fetal Lung	lung
11	chr3:48573600-48592600	Weak transcription	NHDF-Ad	bronchial
12	chr3:48573600-48593400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr3:48574200-48586000	Weak transcription	Primary T cells from cord blood	blood
14	chr3:48574400-48591400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:48574800-48591200	Weak transcription	Dnd41	blood
16	chr3:48576000-48594000	Weak transcription	Small Intestine	intestine
17	chr3:48576400-48590200	Weak transcription	Colonic Mucosa	Colon
18	chr3:48576400-48591800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:48577600-48586400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr3:48577600-48589600	Weak transcription	Gastric	stomach
21	chr3:48577600-48591600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr3:48578000-48593400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr3:48579200-48586200	Strong transcription	Duodenum Mucosa	Duodenum
24	chr3:48579800-48586000	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr3:48581000-48586000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr3:48581000-48591000	Weak transcription	Lung	lung
27	chr3:48581000-48593600	Weak transcription	Right Atrium	heart
28	chr3:48581200-48584000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr3:48581200-48586000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr3:48581200-48586000	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr3:48581200-48586200	Weak transcription	Adipose Nuclei	Adipose
32	chr3:48581200-48586400	Weak transcription	Pancreas	Pancrea
33	chr3:48581200-48589400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr3:48581200-48593600	Weak transcription	Right Ventricle	heart
35	chr3:48581200-48593800	Weak transcription	Ovary	ovary
36	chr3:48581400-48589600	Weak transcription	HSMMtube	muscle
37	chr3:48581400-48591600	Weak transcription	Hela-S3	cervix
38	chr3:48581400-48592800	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr3:48582600-48584800	Weak transcription	Fetal Heart	heart
40	chr3:48582600-48591800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:48582800-48583800	Strong transcription	Brain Substantia Nigra	brain
42	chr3:48582800-48584000	Genic enhancers	HepG2	liver
43	chr3:48582800-48585800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr3:48582800-48585800	Strong transcription	NHLF	lung
45	chr3:48582800-48586000	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr3:48582800-48586600	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr3:48583000-48586000	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr3:48583000-48586200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr3:48583000-48587800	Strong transcription	Brain Germinal Matrix	brain
50	chr3:48583200-48584000	Strong transcription	Brain Hippocampus Middle	brain

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