Variant report

Variant	rs2925754
Chromosome Location	chr2:161060315-161060316
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr2:161060038-161060425	ECC-1	luminal epithelium:	n/a	chr2:161060196-161060205
2	REST	chr2:161060017-161060421	ECC-1	luminal epithelium:	n/a	chr2:161060196-161060205

No.	Distal block	Cell Line	Cell type
1	chr2:161057163..161059631-chr2:161060006..161062265,2	K562	blood:
2	chr2:160968652..160971180-chr2:161059515..161062161,2	MCF-7	breast:
3	chr2:161047917..161051617-chr2:161059788..161062483,3	K562	blood:

Variant related genes	Relation type
ITGB6	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10497212	0.83[GIH][hapmap];0.81[LWK][hapmap];0.81[TSI][hapmap]
rs13393480	0.86[CHB][hapmap];0.86[JPT][hapmap];0.83[LWK][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1563573	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16844790	0.88[GIH][hapmap];0.87[TSI][hapmap]
rs2357770	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2357771	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2357864	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2925752	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2966385	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3101040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3111395	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3111397	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]
rs4665146	0.81[TSI][hapmap]
rs4665164	0.87[ASN][1000 genomes]
rs62175383	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62175385	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62175389	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62175390	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62175433	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6750639	0.84[ASN][1000 genomes]
rs7603686	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.85[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:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:161029400-161063200	Weak transcription	Fetal Muscle Leg	muscle
2	chr2:161048600-161061600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:161050400-161061200	Weak transcription	Esophagus	oesophagus
4	chr2:161051800-161064600	Weak transcription	Lung	lung
5	chr2:161052200-161064600	Weak transcription	Gastric	stomach
6	chr2:161053200-161064600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:161055800-161061400	Weak transcription	Stomach Mucosa	stomach
8	chr2:161056800-161061600	Weak transcription	Colonic Mucosa	Colon
9	chr2:161056800-161061600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr2:161057000-161061000	Weak transcription	NHEK	skin
11	chr2:161057000-161061400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr2:161057000-161061800	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr2:161057000-161062400	Enhancers	HMEC	breast
14	chr2:161057600-161064200	Weak transcription	Fetal Intestine Large	intestine
15	chr2:161058200-161063200	Enhancers	Placenta Amnion	Placenta Amnion
16	chr2:161058400-161061600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr2:161058400-161062400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:161059000-161061200	Weak transcription	NH-A	brain
19	chr2:161059200-161061200	Weak transcription	HSMM	muscle
20	chr2:161059200-161065200	Weak transcription	Psoas Muscle	Psoas
21	chr2:161059400-161061600	Weak transcription	HSMMtube	muscle
22	chr2:161059400-161061800	Weak transcription	Aorta	Aorta
23	chr2:161059600-161061000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr2:161059600-161068000	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr2:161059800-161060600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr2:161059800-161060600	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr2:161060000-161062600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr2:161060000-161066200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:161060200-161060600	ZNF genes & repeats	GM12878-XiMat	blood
30	chr2:161060200-161061400	Enhancers	A549	lung
31	chr2:161060200-161061800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr2:161060200-161062600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr2:161060200-161062600	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr2:161060200-161062800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr2:161060200-161066800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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