Variant report

Variant	rs4241687
Chromosome Location	chr4:69018681-69018682
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:69012983..69014956-chr4:69018521..69020057,2	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10004940	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs10006714	0.86[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]
rs10017410	0.85[CHB][hapmap]
rs10019959	0.83[CHB][hapmap]
rs10024312	0.87[CHB][hapmap]
rs10025371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10026816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10030708	0.82[CHB][hapmap]
rs10031258	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10031769	0.86[CHB][hapmap]
rs11131734	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11930052	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11942083	0.82[CHB][hapmap]
rs11943580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11943765	0.86[CHB][hapmap]
rs11946540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12648613	0.81[CHB][hapmap]
rs13107652	0.82[CHB][hapmap]
rs1370834	0.86[CHB][hapmap]
rs1438413	0.83[EUR][1000 genomes]
rs1561384	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs2874080	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4593187	0.82[CHB][hapmap]
rs4860900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4860902	0.83[CHB][hapmap]
rs60312814	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6552135	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs6552148	0.86[CHB][hapmap]
rs6810773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6818285	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6818664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6819686	0.83[CHB][hapmap]
rs6829596	1.00[CEU][hapmap]
rs6831923	0.87[CHB][hapmap]
rs6845798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7665380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7676484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7682081	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7687396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs961736	0.87[CHB][hapmap]
rs9999396	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879219	chr4:68743032-69028913	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	esv2759257	chr4:68777006-69028913	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	esv1806791	chr4:68781695-69018980	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	esv1808905	chr4:68782651-69020080	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv1814820	chr4:68789778-69033099	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	esv1805370	chr4:68789778-69043722	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	esv2757060	chr4:68790864-69028913	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	esv1812856	chr4:68791333-69021023	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv1008084	chr4:68797598-69482831	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
10	nsv537131	chr4:68797598-69482831	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
11	nsv879221	chr4:68915798-69033099	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
12	esv1812438	chr4:68943858-69154222	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	esv1806586	chr4:68943858-69592846	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
14	nsv879222	chr4:68958980-69022380	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	esv3400302	chr4:69008235-69034717	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4241687	GCOM2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:69013000-69020400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:69014800-69028000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:69017200-69018800	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr4:69017200-69019000	Enhancers	NHEK	skin
5	chr4:69017400-69018800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:69017600-69018800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:69017600-69018800	Enhancers	Placenta Amnion	Placenta Amnion
8	chr4:69017600-69018800	Enhancers	HMEC	breast
9	chr4:69018600-69019200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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