Variant report

Variant	rs7688899
Chromosome Location	chr4:86594600-86594601
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:86591944..86594677-chr4:86595648..86598100,2	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10000472	0.81[CHD][hapmap]
rs10003669	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1031988	0.81[CHD][hapmap]
rs11931290	0.86[CHB][hapmap]
rs11937452	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11943623	0.88[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs12502332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12504294	0.81[CHD][hapmap]
rs12506009	0.81[CHD][hapmap]
rs12506145	0.88[CHB][hapmap]
rs12506596	0.81[CHD][hapmap]
rs12640411	0.81[CHD][hapmap]
rs12644260	0.81[CHD][hapmap]
rs13103706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13106652	0.88[CHB][hapmap];0.89[ASN][1000 genomes]
rs13123541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13129615	0.82[CHB][hapmap];0.84[ASN][1000 genomes]
rs13131183	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13149991	0.88[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs1384132	0.81[CHD][hapmap]
rs1384134	0.81[CHD][hapmap]
rs1384135	0.81[CHD][hapmap]
rs1471605	0.82[CHB][hapmap]
rs1482089	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1564559	0.88[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs1905084	0.89[CHB][hapmap]
rs2062100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28481407	0.81[CHD][hapmap]
rs2869361	0.89[ASN][1000 genomes]
rs2904073	0.89[CHB][hapmap]
rs4693120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4693122	0.81[CHD][hapmap]
rs4693711	0.96[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4693712	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4693716	0.81[CHD][hapmap]
rs4693718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4693719	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4693720	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6531839	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6815397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6849280	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7664042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs766570	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7669879	0.89[CHB][hapmap]
rs7671404	0.89[CHB][hapmap]
rs7681100	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7681661	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7694594	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs979337	0.81[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.81[TSI][hapmap];0.83[ASN][1000 genomes]
rs9884932	0.81[CHD][hapmap]
rs9994722	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9997730	0.88[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461566	chr4:85988032-86725502	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv594747	chr4:85988032-86725502	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
3	nsv470048	chr4:85998783-86720838	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	esv3450999	chr4:86485840-86773745	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
5	nsv829999	chr4:86500257-86666019	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7688899	ARHGAP24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86589000-86601600	Weak transcription	HSMMtube	muscle
2	chr4:86590000-86604600	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr4:86591400-86619400	Weak transcription	Pancreas	Pancrea
4	chr4:86592000-86597600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr4:86592200-86595400	Enhancers	NHDF-Ad	bronchial
6	chr4:86592800-86594600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr4:86592800-86594800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr4:86593000-86595000	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr4:86593000-86595000	Genic enhancers	Primary B cells from cord blood	blood
10	chr4:86593200-86597400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr4:86593600-86596000	Enhancers	GM12878-XiMat	blood
12	chr4:86594000-86594600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr4:86594000-86594600	Enhancers	Primary hematopoietic stem cells	blood
14	chr4:86594000-86595400	Weak transcription	Fetal Stomach	stomach
15	chr4:86594000-86595600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr4:86594000-86595600	Enhancers	Primary B cells from peripheral blood	blood
17	chr4:86594000-86596800	Weak transcription	Left Ventricle	heart
18	chr4:86594000-86597800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr4:86594200-86594600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr4:86594200-86596200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr4:86594400-86595200	Weak transcription	Fetal Muscle Leg	muscle
22	chr4:86594400-86596000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr4:86594400-86596400	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr4:86594400-86596400	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr4:86594400-86596600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr4:86594400-86598400	Weak transcription	Right Atrium	heart
27	chr4:86594400-86601400	Weak transcription	Spleen	Spleen
28	chr4:86594400-86601600	Weak transcription	HSMM	muscle
29	chr4:86594600-86594800	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr4:86594600-86595000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr4:86594600-86597600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr4:86594600-86600000	Weak transcription	Primary hematopoietic stem cells	blood

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