Variant report

Variant	rs12802242
Chromosome Location	chr11:5390446-5390447
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	11:5390022-5391947..11:5700314-5707362	H1-hESC	embryonic stem cell:	embryo
2	11:5250847-5268367..11:5390022-5391947	Hela-S3	cervix:
3	11:5390022-5391947..11:5721056-5732713	H1-hESC	embryonic stem cell:	embryo

Variant related genes	Relation type
ENSG00000132274	Chromatin interaction
ENSG00000260629	Chromatin interaction
ENSG00000223609	Chromatin interaction
ENSG00000132256	Chromatin interaction
ENSG00000229988	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10500635	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10500636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11036919	1.00[JPT][hapmap]
rs11036928	1.00[JPT][hapmap]
rs11826587	1.00[JPT][hapmap]
rs12808928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16930124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17355388	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs17355626	1.00[CHB][hapmap]
rs2647597	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2647608	1.00[CHB][hapmap]
rs2736552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4094102	0.83[CEU][hapmap]
rs4243954	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4243956	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4243958	1.00[JPT][hapmap]
rs4243959	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4296065	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4300412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4306312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4338558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4347419	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs4369438	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4373970	1.00[JPT][hapmap]
rs4439540	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4462380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4494330	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4910752	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs4910755	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4910756	1.00[JPT][hapmap]
rs4910761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4910764	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs4910775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4910776	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4910780	1.00[JPT][hapmap]
rs5006882	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs5006883	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs5006884	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs5006885	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs5006886	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs5006889	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs5024042	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7112862	1.00[JPT][hapmap]
rs7113385	1.00[JPT][hapmap]
rs7113565	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs7113817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7117560	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7131367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7483122	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7929412	1.00[JPT][hapmap]
rs7948662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv524400	chr11:5328361-5416622	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv1048608	chr11:5328516-5645179	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
3	nsv1046068	chr11:5335943-6063742	Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
4	nsv896931	chr11:5357881-5505149	Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
5	nsv832057	chr11:5375585-5576200	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
6	nsv983147	chr11:5376861-5392760	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:5384200-5391200	Enhancers	NHLF	lung
2	chr11:5384200-5391200	Enhancers	Osteobl	bone
3	chr11:5385000-5391400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr11:5386000-5391200	Enhancers	NHDF-Ad	bronchial
5	chr11:5389000-5390600	Weak transcription	HSMMtube	muscle
6	chr11:5389400-5391200	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr11:5389600-5390600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr11:5389600-5390800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr11:5389800-5391200	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr11:5389800-5391200	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr11:5390400-5392000	Weak transcription	K562	blood

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