Variant report

Variant	rs11890990
Chromosome Location	chr2:160970934-160970935
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	SETDB1	chr2:160970750-160971090	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:160968652..160971180-chr2:161059515..161062161,2	MCF-7	breast:
2	chr2:160969263..160971954-chr2:161084180..161086609,2	MCF-7	breast:
3	chr2:160969923..160971430-chr2:161063576..161065947,2	MCF-7	breast:

Variant related genes	Relation type
ITGB6	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs2357863	1.00[MEX][hapmap]
rs2667034	1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs2925764	1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap]
rs2925765	1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap]
rs2966388	0.89[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap]
rs3111394	1.00[YRI][hapmap]
rs56082404	0.99[AFR][1000 genomes]
rs59101427	1.00[AMR][1000 genomes]
rs6715928	1.00[AMR][1000 genomes]
rs6724949	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73967991	1.00[AMR][1000 genomes]
rs73968013	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73968024	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73968047	0.83[AFR][1000 genomes]
rs7602804	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7606596	1.00[MEX][hapmap]
rs925408	1.00[AMR][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	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	nsv875346	chr2:160965335-161044155	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	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	chr2:160954600-160993000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr2:160957400-160981200	Weak transcription	Lung	lung
3	chr2:160959200-161004200	Weak transcription	Gastric	stomach
4	chr2:160959400-160985200	Weak transcription	Esophagus	oesophagus
5	chr2:160959400-161032800	Weak transcription	Psoas Muscle	Psoas
6	chr2:160962800-160971000	Strong transcription	Placenta Amnion	Placenta Amnion
7	chr2:160964200-160993600	Weak transcription	Fetal Muscle Leg	muscle
8	chr2:160964400-160993600	Weak transcription	Fetal Intestine Large	intestine
9	chr2:160966400-160980200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr2:160967200-160979000	Weak transcription	HSMM	muscle
11	chr2:160968200-160971000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:160968600-160977400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:160969000-160983000	Weak transcription	Fetal Intestine Small	intestine
14	chr2:160969200-160982000	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr2:160969600-160971000	Strong transcription	HMEC	breast
16	chr2:160970200-160971200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr2:160970400-160971000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr2:160970400-160971000	Enhancers	NHDF-Ad	bronchial
19	chr2:160970600-160971000	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr2:160970800-160971000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
21	chr2:160970800-160971000	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr2:160970800-160971000	Enhancers	Stomach Mucosa	stomach
23	chr2:160970800-160971200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr2:160970800-160971600	Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr2:160970800-160977600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr2:160970800-160977600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr2:160970800-160978200	Weak transcription	NHEK	skin

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