Variant report

Variant	rs3111397
Chromosome Location	chr2:161051363-161051364
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	chr2:161047148..161049457-chr2:161049468..161051501,2	MCF-7	breast:
2	chr2:161047917..161051617-chr2:161059788..161062483,3	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1037694	0.87[CHB][hapmap];0.86[JPT][hapmap];0.94[YRI][hapmap];0.82[ASN][1000 genomes]
rs10497212	0.87[ASW][hapmap];0.87[CHB][hapmap];0.83[GIH][hapmap];0.84[LWK][hapmap];0.81[TSI][hapmap]
rs13393480	0.81[LWK][hapmap];0.80[ASN][1000 genomes]
rs1563573	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16844790	0.87[ASW][hapmap];0.87[CHB][hapmap];0.88[GIH][hapmap];0.87[LWK][hapmap];0.88[MKK][hapmap];0.87[TSI][hapmap]
rs16844802	0.87[CHB][hapmap]
rs17284082	0.87[CHB][hapmap]
rs2357770	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2357771	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2357864	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2925752	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2925754	0.87[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2966385	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3101040	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3111395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4076843	0.81[YRI][hapmap]
rs4665146	0.81[TSI][hapmap]
rs4665154	0.82[YRI][hapmap]
rs4665156	0.86[CHB][hapmap]
rs4665164	0.80[ASN][1000 genomes]
rs62175383	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62175385	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62175389	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62175390	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62175433	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6432608	0.86[ASN][1000 genomes]
rs7581712	0.87[CHB][hapmap]
rs7603686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]

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	nsv459929	chr2:160963603-161079435	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv583497	chr2:160963603-161079435	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1001502	chr2:160967864-161079450	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:161027200-161051400	Weak transcription	Gastric	stomach
2	chr2:161029400-161063200	Weak transcription	Fetal Muscle Leg	muscle
3	chr2:161045400-161051400	Weak transcription	Fetal Intestine Small	intestine
4	chr2:161047200-161058800	Weak transcription	Psoas Muscle	Psoas
5	chr2:161047400-161053200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:161048600-161061600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr2:161049000-161053600	Genic enhancers	NHEK	skin
8	chr2:161049600-161053800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr2:161049600-161055600	Weak transcription	Fetal Stomach	stomach
10	chr2:161049800-161055200	Weak transcription	Colonic Mucosa	Colon
11	chr2:161050000-161052200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr2:161050000-161052200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:161050400-161051400	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr2:161050400-161051600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:161050400-161053200	Genic enhancers	HMEC	breast
16	chr2:161050400-161061200	Weak transcription	Esophagus	oesophagus
17	chr2:161051000-161051800	Enhancers	Hela-S3	cervix
18	chr2:161051000-161052000	Strong transcription	Skeletal Muscle Male	skeletal muscle
19	chr2:161051000-161052000	Strong transcription	HSMM	muscle
20	chr2:161051000-161052200	Strong transcription	Fetal Intestine Large	intestine
21	chr2:161051000-161052200	Enhancers	Dnd41	blood
22	chr2:161051000-161052400	Genic enhancers	Placenta Amnion	Placenta Amnion
23	chr2:161051000-161052800	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr2:161051000-161052800	Strong transcription	HSMMtube	muscle
25	chr2:161051200-161051800	Enhancers	Stomach Mucosa	stomach
26	chr2:161051200-161052400	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr2:161051200-161052800	Strong transcription	Duodenum Mucosa	Duodenum

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