Variant report

Variant	rs1960329
Chromosome Location	chr2:98422296-98422297
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:98421847..98423499-chr2:98610815..98612996,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000075568	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10166513	0.94[ASN][1000 genomes]
rs10167772	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10168543	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10168709	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10169155	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10175129	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10176826	1.00[CEU][hapmap];0.84[CHB][hapmap]
rs10180434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10180837	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10183768	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10184393	0.82[EUR][1000 genomes]
rs10184457	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs10184552	0.83[AFR][1000 genomes]
rs10188497	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10188713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10189414	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10191101	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10191483	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10192322	0.88[CEU][hapmap];0.82[CHB][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10202138	0.94[ASN][1000 genomes]
rs10206684	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10208070	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10209970	0.88[ASN][1000 genomes]
rs10210520	1.00[ASN][1000 genomes]
rs10210880	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs11886417	0.88[ASN][1000 genomes]
rs11893437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11894541	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11894895	1.00[ASN][1000 genomes]
rs11895170	1.00[CEU][hapmap];0.84[CHB][hapmap]
rs11897301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12712117	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12712120	1.00[ASN][1000 genomes]
rs12712147	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12712162	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12712163	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12712172	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12991122	0.86[AMR][1000 genomes]
rs12992955	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13000585	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13004862	0.89[ASN][1000 genomes]
rs13008678	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13008904	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13010004	1.00[ASN][1000 genomes]
rs13012645	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13387725	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13404788	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13427422	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1446327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1503202	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1982336	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2121271	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2293679	1.00[CEU][hapmap];0.84[CHB][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2305142	0.83[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34190123	0.94[ASN][1000 genomes]
rs34305873	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34414288	1.00[ASN][1000 genomes]
rs34469351	0.84[ASN][1000 genomes]
rs35185431	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35203092	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35402416	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35776557	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35807655	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35940587	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs36079497	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3821053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55753459	0.94[ASN][1000 genomes]
rs6543088	1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs6543111	0.97[ASN][1000 genomes]
rs6707719	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6707750	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6712078	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6713504	0.80[EUR][1000 genomes]
rs6718982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6721323	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6728312	1.00[ASN][1000 genomes]
rs6736735	0.83[CEU][hapmap]
rs6738401	0.94[ASN][1000 genomes]
rs6751727	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6755021	0.94[ASN][1000 genomes]
rs6756969	0.88[ASN][1000 genomes]
rs6760008	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs68115667	0.88[ASN][1000 genomes]
rs6875	1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs71429373	0.94[ASN][1000 genomes]
rs718159	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7557495	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7570009	1.00[ASN][1000 genomes]
rs7578638	0.88[ASN][1000 genomes]
rs7582298	0.94[ASN][1000 genomes]
rs7588227	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7591374	0.83[EUR][1000 genomes]
rs7593290	1.00[ASN][1000 genomes]
rs7594928	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7595039	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7599043	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7605288	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9784011	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9808558	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9973490	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531382	chr2:98250628-98457616	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS 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	28 gene(s)	inside rSNPs	diseases
2	nsv526360	chr2:98403683-98814054	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv521568	chr2:98403683-98826203	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98387800-98438200	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr2:98399600-98429600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:98401400-98422600	Strong transcription	Primary B cells from cord blood	blood
4	chr2:98401600-98422400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr2:98402000-98423200	Strong transcription	Primary B cells from peripheral blood	blood
6	chr2:98402000-98440400	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr2:98402200-98422600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:98402400-98428600	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr2:98402600-98422600	Strong transcription	Liver	Liver
10	chr2:98403200-98422400	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr2:98403600-98422600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:98405800-98459600	Weak transcription	Stomach Mucosa	stomach
13	chr2:98406200-98427200	Weak transcription	K562	blood
14	chr2:98406400-98469200	Weak transcription	A549	lung
15	chr2:98409000-98425000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr2:98409200-98423600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr2:98409400-98423400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr2:98409400-98423600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr2:98409400-98423600	Weak transcription	Psoas Muscle	Psoas
20	chr2:98409400-98484200	Weak transcription	HUVEC	blood vessel
21	chr2:98409600-98429800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr2:98409800-98425000	Weak transcription	Fetal Brain Female	brain
23	chr2:98409800-98485000	Weak transcription	Hela-S3	cervix
24	chr2:98410000-98423400	Weak transcription	Right Ventricle	heart
25	chr2:98410000-98424800	Weak transcription	Brain Germinal Matrix	brain
26	chr2:98410000-98424800	Weak transcription	Esophagus	oesophagus
27	chr2:98410000-98425200	Weak transcription	Gastric	stomach
28	chr2:98410000-98425400	Weak transcription	Pancreas	Pancrea
29	chr2:98410000-98425800	Weak transcription	NH-A	brain
30	chr2:98410000-98427000	Weak transcription	Brain Angular Gyrus	brain
31	chr2:98410000-98427200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr2:98410000-98427200	Weak transcription	Brain Substantia Nigra	brain
33	chr2:98410000-98427400	Weak transcription	HSMMtube	muscle
34	chr2:98410000-98427800	Weak transcription	Spleen	Spleen
35	chr2:98410000-98435800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr2:98410000-98446000	Weak transcription	Colonic Mucosa	Colon
37	chr2:98410000-98456200	Weak transcription	Thymus	Thymus
38	chr2:98410000-98456800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr2:98410000-98456800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr2:98410000-98457400	Weak transcription	Small Intestine	intestine
41	chr2:98410200-98427200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr2:98410800-98432000	Weak transcription	Fetal Intestine Small	intestine
43	chr2:98411000-98429200	Strong transcription	HSMM	muscle
44	chr2:98411400-98427200	Weak transcription	Fetal Brain Male	brain
45	chr2:98412400-98422600	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr2:98412600-98422400	Strong transcription	Placenta	Placenta
47	chr2:98413000-98422600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr2:98414200-98422600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr2:98414200-98422600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr2:98414200-98426200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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