Variant report

Variant	rs11930449
Chromosome Location	chr4:86498937-86498938
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	chr4:86497689..86499255-chr4:86523106..86525131,2	K562	blood:
2	chr4:86497193..86499819-chr4:86506263..86509883,3	K562	blood:

Extended variants
information (count: 82 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10000472	0.90[CEU][hapmap];0.90[CHB][hapmap];0.96[MEX][hapmap]
rs10017042	0.90[CEU][hapmap];0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs10018069	0.90[CEU][hapmap]
rs10018546	0.95[CEU][hapmap]
rs10020489	0.80[MEX][hapmap]
rs10028585	0.90[CEU][hapmap]
rs1031988	0.90[CEU][hapmap];0.90[CHB][hapmap];0.92[MEX][hapmap]
rs10454245	0.90[CEU][hapmap];0.90[CHB][hapmap]
rs11097059	0.87[MEX][hapmap]
rs1161259	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12501951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12504294	0.90[CEU][hapmap];0.90[CHB][hapmap];0.96[MEX][hapmap]
rs12506009	0.90[CEU][hapmap];0.90[CHB][hapmap];0.92[MEX][hapmap]
rs12506100	0.90[CEU][hapmap];0.90[CHB][hapmap]
rs12506145	0.90[CEU][hapmap];0.89[CHB][hapmap]
rs12506596	0.90[CEU][hapmap];0.90[CHB][hapmap];0.92[MEX][hapmap];0.85[ASN][1000 genomes]
rs12509634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12640411	0.90[CEU][hapmap];0.90[CHB][hapmap];0.92[MEX][hapmap]
rs12644260	0.90[CEU][hapmap];0.90[CHB][hapmap];0.96[MEX][hapmap]
rs12644694	0.90[CEU][hapmap]
rs12644703	0.90[CEU][hapmap];0.80[CHB][hapmap]
rs12650652	0.90[CEU][hapmap];0.89[CHB][hapmap]
rs13103706	0.82[MEX][hapmap]
rs13104640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1351551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1384132	0.90[CEU][hapmap];0.90[CHB][hapmap];0.96[MEX][hapmap]
rs1384134	0.90[CEU][hapmap];0.90[CHB][hapmap]
rs1384135	0.90[CEU][hapmap];0.90[CHB][hapmap];0.92[MEX][hapmap]
rs1384136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1384137	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1471605	0.89[CEU][hapmap];0.84[CHB][hapmap]
rs1600840	0.90[CHB][hapmap]
rs17387344	0.80[MEX][hapmap]
rs17388899	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17389300	0.90[CEU][hapmap];0.90[CHB][hapmap];0.92[MEX][hapmap];0.85[ASN][1000 genomes]
rs17389342	0.82[ASN][1000 genomes]
rs1871823	0.88[AFR][1000 genomes]
rs1905083	0.90[CEU][hapmap];0.89[CHB][hapmap]
rs1905084	0.90[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap]
rs2128100	0.87[MEX][hapmap]
rs28481407	0.90[CEU][hapmap];0.90[CHB][hapmap];0.96[MEX][hapmap]
rs2869363	0.90[CEU][hapmap];0.90[CHB][hapmap]
rs28719006	0.82[ASN][1000 genomes]
rs2904069	0.81[GIH][hapmap]
rs2904073	0.90[CEU][hapmap];0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs4450919	0.94[CEU][hapmap];0.89[CHB][hapmap];0.82[ASN][1000 genomes]
rs4693118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4693120	0.83[MEX][hapmap]
rs4693122	0.90[CEU][hapmap];0.90[CHB][hapmap];0.96[MEX][hapmap]
rs4693124	0.90[CEU][hapmap];0.90[CHB][hapmap]
rs4693708	0.87[AFR][1000 genomes]
rs4693710	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4693712	0.83[MEX][hapmap]
rs4693716	0.90[CEU][hapmap];0.90[CHB][hapmap];0.92[MEX][hapmap];0.82[ASN][1000 genomes]
rs4693719	0.83[MEX][hapmap]
rs59940085	0.82[ASN][1000 genomes]
rs62315648	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62317179	0.85[ASN][1000 genomes]
rs62317184	0.82[ASN][1000 genomes]
rs6531847	0.90[CEU][hapmap]
rs6815397	0.83[MEX][hapmap]
rs6817114	0.90[CEU][hapmap];0.90[CHB][hapmap]
rs6817221	0.90[CEU][hapmap];0.88[CHB][hapmap]
rs6817542	0.90[CEU][hapmap];0.90[CHB][hapmap]
rs6817549	0.90[CEU][hapmap];0.89[CHB][hapmap]
rs6821858	0.81[GIH][hapmap]
rs72613142	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72613143	0.85[ASN][1000 genomes]
rs7655020	0.86[CEU][hapmap]
rs7669879	0.90[CEU][hapmap];0.90[CHB][hapmap]
rs7671404	0.90[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap]
rs7672353	0.90[CEU][hapmap];0.90[CHB][hapmap]
rs7683928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7695028	0.83[ASN][1000 genomes]
rs9760558	0.81[GIH][hapmap]
rs9884932	0.90[CEU][hapmap];0.90[CHB][hapmap];0.96[MEX][hapmap];0.82[ASN][1000 genomes]
rs9997730	0.90[CEU][hapmap];0.89[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	nsv519588	chr4:85762385-86591202	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11930449	ARHGAP24	cis	lymphoblastoid	seeQTL
rs11930449	ARHGAP24	Cis_1M	lymphoblastoid	RTeQTL
rs11930449	SPARCL1	cis	cerebellum	SCAN
rs11930449	PKD2	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86478000-86501000	Weak transcription	Right Ventricle	heart
2	chr4:86486000-86509200	Weak transcription	Left Ventricle	heart
3	chr4:86487000-86509200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:86487200-86521200	Weak transcription	HSMMtube	muscle
5	chr4:86488800-86512400	Weak transcription	Fetal Muscle Trunk	muscle
6	chr4:86492200-86502000	Strong transcription	Primary B cells from peripheral blood	blood
7	chr4:86492600-86501400	Weak transcription	Fetal Muscle Leg	muscle
8	chr4:86492600-86517000	Weak transcription	Adipose Nuclei	Adipose
9	chr4:86494400-86501200	Weak transcription	Primary B cells from cord blood	blood
10	chr4:86495000-86516200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr4:86495200-86512200	Weak transcription	NHDF-Ad	bronchial
12	chr4:86497000-86499400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr4:86497200-86499000	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr4:86497200-86500000	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr4:86497200-86501200	Active TSS	K562	blood
16	chr4:86497400-86499000	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr4:86497400-86501200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr4:86497400-86516800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr4:86498800-86501200	Weak transcription	HSMM	muscle
20	chr4:86498800-86512400	Weak transcription	Psoas Muscle	Psoas

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