Variant report

Variant	rs1561476
Chromosome Location	chr2:111787027-111787028
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:111785222..111792269-chr2:111873385..111881089,20	MCF-7	breast:
2	chr2:111786662..111788456-chr2:111876359..111879256,2	MCF-7	breast:
3	chr2:111786376..111787035-chr2:111873340..111875017,8	MCF-7	breast:
4	chr2:111786327..111787920-chr2:111880079..111881845,2	MCF-7	breast:
5	chr2:111785810..111788620-chr2:111868172..111870697,2	MCF-7	breast:
6	chr2:111786376..111787935-chr2:111803727..111805483,2	MCF-7	breast:
7	chr2:111786604..111788790-chr2:111806791..111809985,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153094	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10180604	0.81[ASN][1000 genomes]
rs10183720	0.82[CEU][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1157083	0.82[CEU][hapmap];0.81[ASN][1000 genomes]
rs1157084	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs1157455	0.82[CEU][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11679341	0.82[CEU][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11685628	0.82[ASN][1000 genomes]
rs1384790	0.82[CEU][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1384793	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1384795	0.82[CEU][hapmap];0.82[GIH][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1384796	0.81[CEU][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1471691	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs1483533	0.82[CEU][hapmap];0.90[GIH][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1483535	0.82[CEU][hapmap];0.90[GIH][hapmap];0.82[ASN][1000 genomes]
rs1561477	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.93[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]
rs1837371	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1842981	0.82[CEU][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2062221	0.80[EUR][1000 genomes]
rs2062225	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs2128813	0.82[CEU][hapmap];0.90[GIH][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs323648	0.80[EUR][1000 genomes]
rs3789093	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs3789095	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs4848367	0.82[CEU][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4849340	0.82[CEU][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6419551	0.80[EUR][1000 genomes]
rs6542248	0.82[CEU][hapmap];0.90[GIH][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6722913	0.82[CEU][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6731964	0.82[CEU][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6733493	0.82[CEU][hapmap];0.90[GIH][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6733497	0.91[CEU][hapmap];0.81[EUR][1000 genomes];0.83[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	nsv874838	chr2:111376870-112046226	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv874839	chr2:111400934-111868010	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv834330	chr2:111593290-111789447	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:111775200-111787800	Weak transcription	Spleen	Spleen
2	chr2:111784600-111787400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:111785000-111787600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr2:111785600-111790200	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr2:111786000-111795800	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr2:111786200-111792400	Enhancers	Fetal Lung	lung
7	chr2:111786400-111788200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:111786400-111790400	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr2:111786600-111787800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:111786600-111788000	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr2:111786600-111788200	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr2:111786600-111788600	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr2:111786600-111790600	Enhancers	Duodenum Mucosa	Duodenum
14	chr2:111786800-111787800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr2:111786800-111788000	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr2:111786800-111788000	Enhancers	Primary B cells from cord blood	blood
17	chr2:111786800-111788200	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr2:111786800-111788200	Enhancers	Placenta	Placenta
19	chr2:111786800-111790000	Enhancers	Rectal Mucosa Donor 29	rectum
20	chr2:111786800-111792800	Enhancers	Fetal Intestine Small	intestine
21	chr2:111787000-111787400	Enhancers	H1 Cell Line	embryonic stem cell
22	chr2:111787000-111787400	Enhancers	Dnd41	blood
23	chr2:111787000-111788000	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr2:111787000-111788200	Enhancers	H9 Cell Line	embryonic stem cell
25	chr2:111787000-111788200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr2:111787000-111788200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr2:111787000-111788200	Enhancers	Fetal Thymus	thymus
28	chr2:111787000-111788600	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr2:111787000-111788600	Enhancers	Colonic Mucosa	Colon
30	chr2:111787000-111789000	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr2:111787000-111789200	Enhancers	Fetal Heart	heart
32	chr2:111787000-111789800	Enhancers	Fetal Stomach	stomach
33	chr2:111787000-111792000	Enhancers	Stomach Mucosa	stomach
34	chr2:111787000-111792800	Enhancers	Fetal Intestine Large	intestine

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