Variant report

Variant	rs10172841
Chromosome Location	chr2:101025811-101025812
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:101021035..101023406-chr2:101025685..101028332,2	MCF-7	breast:
2	chr2:101022665..101026054-chr2:101026732..101029227,3	K562	blood:
3	chr2:101016960..101020223-chr2:101021855..101026333,5	K562	blood:
4	chr2:101025440..101029352-chr2:101031639..101035413,6	K562	blood:

Variant related genes	Relation type
ENSG00000115526	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10176978	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10180685	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10183063	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10193535	0.93[GIH][hapmap]
rs10206374	0.90[GIH][hapmap]
rs1057056	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[ASN][1000 genomes]
rs1057063	0.97[ASN][1000 genomes]
rs1057064	1.00[CHB][hapmap]
rs1124009	1.00[CHB][hapmap];0.93[GIH][hapmap];0.93[ASN][1000 genomes]
rs13400841	0.94[ASW][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.88[MEX][hapmap];0.95[ASN][1000 genomes]
rs1370627	0.93[GIH][hapmap]
rs1437972	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.93[ASN][1000 genomes]
rs1465829	0.85[CHD][hapmap]
rs17024034	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17024035	0.93[GIH][hapmap]
rs17024129	0.93[GIH][hapmap]
rs17024133	0.97[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap]
rs17024136	0.93[GIH][hapmap]
rs17024144	0.93[GIH][hapmap]
rs17024203	0.85[CHD][hapmap]
rs17024207	0.85[CHD][hapmap]
rs17024209	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.88[ASN][1000 genomes]
rs1898573	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs2083148	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2118466	0.88[EUR][1000 genomes]
rs2309801	0.94[ASW][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.88[MEX][hapmap];0.95[ASN][1000 genomes]
rs3748934	0.85[CHD][hapmap]
rs3748936	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[ASN][1000 genomes]
rs3791358	1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4149506	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4149509	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4149514	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.85[LWK][hapmap];0.81[MKK][hapmap];0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4149515	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.82[LWK][hapmap];0.97[ASN][1000 genomes]
rs4149516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4149522	0.85[CHD][hapmap]
rs4850932	0.81[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[ASN][1000 genomes]
rs55932868	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56741959	1.00[ASN][1000 genomes]
rs57862179	0.93[ASN][1000 genomes]
rs58164864	1.00[ASN][1000 genomes]
rs58674788	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59701896	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59858985	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60468180	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60566188	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61710328	1.00[ASN][1000 genomes]
rs6542933	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6542945	0.93[ASN][1000 genomes]
rs6542946	1.00[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6706707	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6725672	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[ASN][1000 genomes]
rs6727379	0.85[TSI][hapmap]
rs6728575	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6732285	0.86[GIH][hapmap]
rs6736938	0.95[ASN][1000 genomes]
rs6738566	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6739589	0.97[ASN][1000 genomes]
rs6749572	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6750040	1.00[CHB][hapmap]
rs6754869	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap];0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6755285	1.00[ASN][1000 genomes]
rs6758515	0.86[AMR][1000 genomes]
rs6758622	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6761084	0.95[ASN][1000 genomes]
rs6761561	0.86[AMR][1000 genomes]
rs73966105	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73966106	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73968413	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7559084	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7561065	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7562184	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7562636	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7562754	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7565502	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7567130	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7571410	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7571651	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7571659	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7575422	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap];1.00[ASN][1000 genomes]
rs7582096	0.94[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[ASN][1000 genomes]
rs7585713	0.94[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap];0.95[ASN][1000 genomes]
rs7585898	0.93[GIH][hapmap]
rs7596483	1.00[ASN][1000 genomes]
rs7598205	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7598227	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7605834	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs876439	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007777	chr2:100816913-101308914	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv535844	chr2:100816913-101308914	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv582531	chr2:100908508-101207639	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv916792	chr2:101021066-101525200	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:101005600-101032800	Weak transcription	HUVEC	blood vessel
2	chr2:101005800-101033000	Weak transcription	Duodenum Mucosa	Duodenum
3	chr2:101006600-101031600	Strong transcription	Fetal Stomach	stomach
4	chr2:101007000-101027200	Strong transcription	Stomach Smooth Muscle	stomach
5	chr2:101007200-101032000	Weak transcription	NHDF-Ad	bronchial
6	chr2:101007600-101030600	Weak transcription	NH-A	brain
7	chr2:101008000-101033000	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr2:101009400-101026400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:101010200-101032800	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr2:101013200-101030400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr2:101013200-101033000	Weak transcription	Fetal Intestine Large	intestine
12	chr2:101014400-101033200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr2:101014800-101032400	Weak transcription	Hela-S3	cervix
14	chr2:101015600-101033000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr2:101016400-101028000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr2:101016400-101032600	Weak transcription	HSMM	muscle
17	chr2:101017000-101032800	Weak transcription	Osteobl	bone
18	chr2:101017400-101026600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:101017400-101026600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr2:101017600-101027000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr2:101018400-101033000	Weak transcription	Primary B cells from cord blood	blood
22	chr2:101019000-101032800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:101020400-101026600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr2:101021000-101033200	Weak transcription	Colonic Mucosa	Colon
25	chr2:101021800-101028200	Weak transcription	K562	blood
26	chr2:101022200-101033000	Weak transcription	HSMMtube	muscle
27	chr2:101022400-101026600	Weak transcription	Esophagus	oesophagus
28	chr2:101022600-101032200	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr2:101022800-101026000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr2:101022800-101027000	Enhancers	Right Atrium	heart
31	chr2:101022800-101030200	Weak transcription	Thymus	Thymus
32	chr2:101022800-101030400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr2:101022800-101030600	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr2:101022800-101032200	Weak transcription	Rectal Smooth Muscle	rectum
35	chr2:101022800-101032400	Weak transcription	Colon Smooth Muscle	Colon
36	chr2:101022800-101033000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr2:101022800-101033000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr2:101023200-101026400	Weak transcription	Lung	lung
39	chr2:101023200-101029400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr2:101023200-101030400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:101023200-101032800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr2:101023200-101033000	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr2:101023200-101033000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr2:101023200-101033000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr2:101023200-101033000	Weak transcription	Fetal Thymus	thymus
46	chr2:101023400-101026600	Weak transcription	Placenta	Placenta
47	chr2:101023400-101032600	Weak transcription	Primary hematopoietic stem cells	blood
48	chr2:101023400-101033000	Weak transcription	Fetal Kidney	kidney
49	chr2:101023600-101027200	Genic enhancers	Brain Germinal Matrix	brain
50	chr2:101023600-101027400	Genic enhancers	Cortex derived primary cultured neurospheres	brain

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