Variant report

Variant	rs11708869
Chromosome Location	chr3:178873855-178873856
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:178872506..178874182-chr3:178879392..178881985,2	K562	blood:
2	chr3:178872310..178876129-chr3:178876945..178878643,3	MCF-7	breast:
3	chr3:178873426..178875261-chr3:178876713..178879813,4	K562	blood:
4	chr3:178872334..178874182-chr3:178879861..178881985,2	K562	blood:
5	chr3:178872111..178873931-chr3:179064322..179066480,2	K562	blood:
6	chr3:178873426..178876051-chr3:178876789..178878414,2	K562	blood:

Variant related genes	Relation type
ENSG00000171109	Chromatin interaction

Extended variants
information (count: 126 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs1059691	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10936992	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10936994	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11706842	1.00[ASN][1000 genomes]
rs11918324	0.97[ASN][1000 genomes]
rs11918587	1.00[ASN][1000 genomes]
rs11919383	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11922631	0.90[ASN][1000 genomes]
rs11924545	0.89[ASN][1000 genomes]
rs11924547	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11924600	0.89[ASN][1000 genomes]
rs11925655	1.00[ASN][1000 genomes]
rs12488074	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1568205	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17849071	0.97[ASN][1000 genomes]
rs1850504	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1970901	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1976765	1.00[ASN][1000 genomes]
rs2865082	0.97[ASN][1000 genomes]
rs3729674	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3729676	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3729682	0.97[ASN][1000 genomes]
rs3729694	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3960984	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3975510	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3975513	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3976507	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4080957	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4855093	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855095	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55685804	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55933053	1.00[ASN][1000 genomes]
rs55961756	0.97[ASN][1000 genomes]
rs56095736	0.90[ASN][1000 genomes]
rs56143971	0.97[ASN][1000 genomes]
rs56372555	1.00[ASN][1000 genomes]
rs56378415	0.95[ASN][1000 genomes]
rs57299654	0.82[ASN][1000 genomes]
rs59340081	1.00[ASN][1000 genomes]
rs59408989	0.95[ASN][1000 genomes]
rs59922883	1.00[ASN][1000 genomes]
rs61796482	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61796483	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62408837	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6443619	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6443624	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6443625	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6443626	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6443627	1.00[ASN][1000 genomes]
rs6443628	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6443629	0.93[ASN][1000 genomes]
rs67562832	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67609137	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6765953	0.97[ASN][1000 genomes]
rs6767284	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6769154	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6769162	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6769508	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6770267	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771313	0.90[ASN][1000 genomes]
rs6774158	0.97[ASN][1000 genomes]
rs6777203	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6782557	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6786114	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6791153	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67920954	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6792189	1.00[ASN][1000 genomes]
rs6794252	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6797304	1.00[ASN][1000 genomes]
rs6798817	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6799756	1.00[ASN][1000 genomes]
rs6803076	0.88[ASN][1000 genomes]
rs6803219	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6806555	1.00[ASN][1000 genomes]
rs6806917	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6810246	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73051974	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73187264	0.97[ASN][1000 genomes]
rs73187276	0.97[ASN][1000 genomes]
rs7372645	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7612533	1.00[ASN][1000 genomes]
rs7614305	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7614418	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7615076	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7621329	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7621436	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7623154	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7624090	0.97[ASN][1000 genomes]
rs7627273	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7628855	1.00[ASN][1000 genomes]
rs7635669	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7636454	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7638323	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7638649	1.00[ASN][1000 genomes]
rs7641889	1.00[ASN][1000 genomes]
rs7641983	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7644648	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7645550	0.82[ASN][1000 genomes]
rs7646409	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7648857	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7650809	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7651265	1.00[ASN][1000 genomes]
rs938752	1.00[ASN][1000 genomes]
rs9631497	0.95[ASN][1000 genomes]
rs9813190	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9819762	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9829903	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9831234	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9833438	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9838411	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9839519	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9841051	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9844270	0.90[ASN][1000 genomes]
rs9844482	0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9850621	1.00[ASN][1000 genomes]
rs9862294	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9866361	0.94[AFR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9877812	1.00[ASN][1000 genomes]
rs9881887	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv461026	chr3:178661814-178886609	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv592649	chr3:178661814-178886609	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	esv1792927	chr3:178734558-178877169	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	esv1841799	chr3:178739594-178884337	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	esv3354111	chr3:178833305-179156908	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:178867200-178878200	Weak transcription	Gastric	stomach
2	chr3:178867600-178878200	Weak transcription	Pancreas	Pancrea
3	chr3:178867600-178882400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:178867600-178883400	Weak transcription	Stomach Mucosa	stomach
5	chr3:178867800-178874000	Weak transcription	Fetal Stomach	stomach
6	chr3:178867800-178878000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:178867800-178878200	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr3:178867800-178878200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr3:178867800-178900200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr3:178868000-178874200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:178868000-178878200	Weak transcription	Right Atrium	heart
12	chr3:178868000-178892400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr3:178868400-178876000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr3:178868600-178874000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr3:178868600-178874000	Weak transcription	Brain Substantia Nigra	brain
16	chr3:178868600-178874000	Weak transcription	HSMMtube	muscle
17	chr3:178868600-178876200	Weak transcription	NHDF-Ad	bronchial
18	chr3:178868600-178881400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:178868600-178893000	Weak transcription	Aorta	Aorta
20	chr3:178868800-178874200	Weak transcription	HSMM	muscle
21	chr3:178869200-178874000	Weak transcription	Brain Angular Gyrus	brain
22	chr3:178869200-178898000	Weak transcription	Primary hematopoietic stem cells	blood
23	chr3:178869400-178874600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr3:178869400-178887200	Weak transcription	Fetal Brain Male	brain
25	chr3:178869600-178874000	Weak transcription	Brain Anterior Caudate	brain
26	chr3:178869600-178874000	Weak transcription	Brain Hippocampus Middle	brain
27	chr3:178869800-178874000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr3:178869800-178874000	Weak transcription	Fetal Kidney	kidney
29	chr3:178869800-178875800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr3:178869800-178877400	Weak transcription	Right Ventricle	heart
31	chr3:178869800-178877800	Weak transcription	Ovary	ovary
32	chr3:178869800-178878200	Weak transcription	Primary B cells from peripheral blood	blood
33	chr3:178869800-178883400	Weak transcription	Liver	Liver
34	chr3:178870000-178874200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:178870000-178880600	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr3:178870400-178874000	Weak transcription	Primary T cells from cord blood	blood
37	chr3:178870400-178874400	Weak transcription	Primary B cells from cord blood	blood
38	chr3:178870600-178874000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:178870600-178874000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr3:178870600-178874000	Weak transcription	HMEC	breast
41	chr3:178870600-178876000	Weak transcription	Fetal Heart	heart
42	chr3:178870800-178875200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr3:178870800-178876000	Weak transcription	GM12878-XiMat	blood
44	chr3:178870800-178896400	Weak transcription	K562	blood
45	chr3:178872000-178874600	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr3:178872000-178876200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr3:178872200-178874000	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr3:178872400-178874000	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr3:178872400-178874600	Weak transcription	Psoas Muscle	Psoas
50	chr3:178872400-178876000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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