Variant report

Variant	rs2006871
Chromosome Location	chr3:48586697-48586698
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:48486933..48489526-chr3:48585390..48587565,2	MCF-7	breast:
2	chr3:48586074..48587895-chr3:48593005..48594952,2	MCF-7	breast:
3	chr3:48572206..48574308-chr3:48584630..48587149,2	MCF-7	breast:
4	chr3:48477195..48477710-chr3:48585832..48586734,2	K562	blood:
5	chr3:48504857..48507014-chr3:48585352..48587793,2	MCF-7	breast:
6	chr3:48540004..48544821-chr3:48582947..48586944,4	MCF-7	breast:
7	chr3:48514614..48515271-chr3:48585932..48586761,2	MCF-7	breast:
8	chr3:48505336..48507903-chr3:48585483..48588642,3	MCF-7	breast:
9	chr3:48584950..48588174-chr3:48591529..48594760,3	K562	blood:
10	chr3:48506855..48508607-chr3:48585951..48588307,2	K562	blood:
11	chr3:48506640..48507542-chr3:48585917..48586810,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000164054	Chromatin interaction
ENSG00000213689	Chromatin interaction
ENSG00000244380	Chromatin interaction
ENSG00000164053	Chromatin interaction
ENSG00000114268	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1003649	0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap]
rs10049154	0.81[ASN][1000 genomes]
rs10470687	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11706983	0.83[GIH][hapmap]
rs11708786	0.83[GIH][hapmap]
rs11719291	0.83[GIH][hapmap]
rs12107252	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs12107418	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs13060933	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13062576	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs13063312	0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs13064619	0.81[ASN][1000 genomes]
rs13070798	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs13091944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs13094578	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs13100178	0.85[ASN][1000 genomes]
rs13319635	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13319651	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13324142	0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs13434258	0.83[GIH][hapmap]
rs17080289	0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes]
rs2276850	0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2276852	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2286652	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2302295	1.00[JPT][hapmap]
rs2310996	0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2854394	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2854395	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28563843	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28581474	0.85[ASN][1000 genomes]
rs35064573	0.83[GIH][hapmap]
rs35562294	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3755819	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3806694	1.00[JPT][hapmap]
rs3821875	1.00[JPT][hapmap]
rs3821876	0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs3969942	0.90[CHD][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.85[ASN][1000 genomes]
rs4075082	0.85[ASN][1000 genomes]
rs6442126	0.86[CHB][hapmap]
rs6442127	0.83[ASN][1000 genomes]
rs6765317	0.81[ASN][1000 genomes]
rs6773261	1.00[JPT][hapmap]
rs6781283	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6785845	0.81[ASN][1000 genomes]
rs6792156	0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6792525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6806059	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6809981	0.80[ASN][1000 genomes]
rs740787	0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs7428949	0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7434077	0.89[CHB][hapmap];0.85[CHD][hapmap];0.85[ASN][1000 genomes]
rs7434107	0.85[ASN][1000 genomes]
rs7620853	1.00[JPT][hapmap]
rs7623614	0.85[ASN][1000 genomes]
rs7631574	0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs7640031	0.85[ASN][1000 genomes]
rs7644771	0.85[ASN][1000 genomes]
rs9810549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9810991	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]
rs9811318	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9812200	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9814951	0.85[GIH][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs9816942	0.85[ASN][1000 genomes]
rs9821797	1.00[JPT][hapmap]
rs9822677	0.81[ASN][1000 genomes]
rs9830581	0.90[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs9835827	0.81[ASN][1000 genomes]
rs9835902	1.00[CEU][hapmap];0.89[CHB][hapmap];0.80[CHD][hapmap];0.85[GIH][hapmap];0.81[TSI][hapmap];0.83[ASN][1000 genomes]
rs9836462	0.84[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9837687	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9841602	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9843316	0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes]
rs9848824	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9849280	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9850102	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9851743	0.85[ASN][1000 genomes]
rs9851771	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.85[ASN][1000 genomes]
rs9864729	0.98[ASN][1000 genomes]
rs9869698	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9871180	1.00[CEU][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9871608	0.85[ASN][1000 genomes]
rs9873726	1.00[JPT][hapmap]
rs9875911	1.00[GIH][hapmap]
rs9878950	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9881877	0.90[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.91[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];0.90[TSI][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

No data

Chromatin state (count:103 , 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	chr3:48562600-48592000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:48570600-48591600	Weak transcription	Fetal Brain Male	brain
5	chr3:48573600-48589600	Weak transcription	Fetal Lung	lung
6	chr3:48573600-48592600	Weak transcription	NHDF-Ad	bronchial
7	chr3:48573600-48593400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr3:48574400-48591400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:48574800-48591200	Weak transcription	Dnd41	blood
10	chr3:48576000-48594000	Weak transcription	Small Intestine	intestine
11	chr3:48576400-48590200	Weak transcription	Colonic Mucosa	Colon
12	chr3:48576400-48591800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr3:48577600-48589600	Weak transcription	Gastric	stomach
14	chr3:48577600-48591600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr3:48578000-48593400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr3:48581000-48591000	Weak transcription	Lung	lung
17	chr3:48581000-48593600	Weak transcription	Right Atrium	heart
18	chr3:48581200-48589400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr3:48581200-48593600	Weak transcription	Right Ventricle	heart
20	chr3:48581200-48593800	Weak transcription	Ovary	ovary
21	chr3:48581400-48589600	Weak transcription	HSMMtube	muscle
22	chr3:48581400-48591600	Weak transcription	Hela-S3	cervix
23	chr3:48581400-48592800	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr3:48582600-48591800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:48583000-48587800	Strong transcription	Brain Germinal Matrix	brain
26	chr3:48583200-48586800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:48583400-48587600	Strong transcription	K562	blood
28	chr3:48583400-48587800	Strong transcription	H9 Cell Line	embryonic stem cell
29	chr3:48583400-48588000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr3:48583400-48588000	Strong transcription	Placenta Amnion	Placenta Amnion
31	chr3:48583400-48588400	Strong transcription	Fetal Brain Female	brain
32	chr3:48583400-48589200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr3:48583400-48590200	Strong transcription	GM12878-XiMat	blood
34	chr3:48583600-48586800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr3:48583600-48591800	Strong transcription	NHEK	skin
36	chr3:48583800-48591600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr3:48584000-48590400	Weak transcription	Esophagus	oesophagus
38	chr3:48584200-48593800	Weak transcription	Aorta	Aorta
39	chr3:48584800-48589400	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr3:48584800-48593600	Weak transcription	NH-A	brain
41	chr3:48585000-48589400	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr3:48585000-48589600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr3:48585000-48591800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr3:48585000-48593400	Weak transcription	HSMM	muscle
45	chr3:48585200-48592600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr3:48585200-48593400	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr3:48585200-48593600	Weak transcription	Osteobl	bone
48	chr3:48585400-48592600	Weak transcription	A549	lung
49	chr3:48585600-48586800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr3:48585600-48587000	Genic enhancers	Fetal Muscle Leg	muscle

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