Variant report

Variant	rs10159302
Chromosome Location	chr1:57805550-57805551
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10493218	1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11207023	1.00[JPT][hapmap]
rs11800574	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11803541	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11805025	1.00[JPT][hapmap]
rs11807631	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1424471	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1424472	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17096836	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17115683	1.00[ASN][1000 genomes]
rs17115713	1.00[JPT][hapmap]
rs17115722	1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17115739	1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs17115757	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17115765	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17115767	1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17115834	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17115844	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1778031	1.00[ASN][1000 genomes]
rs17838097	1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1981891	1.00[ASN][1000 genomes]
rs2805873	1.00[CHB][hapmap]
rs35664891	1.00[ASN][1000 genomes]
rs3738552	1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3850553	1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3850554	0.82[GIH][hapmap];1.00[ASN][1000 genomes]
rs4309005	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4912242	1.00[ASN][1000 genomes]
rs4912243	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs507466	1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs524941	1.00[ASN][1000 genomes]
rs566739	1.00[JPT][hapmap]
rs60790797	1.00[ASN][1000 genomes]
rs6657926	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72909225	1.00[ASN][1000 genomes]
rs72909227	1.00[ASN][1000 genomes]
rs72909233	1.00[ASN][1000 genomes]
rs72909243	1.00[ASN][1000 genomes]
rs72909245	1.00[ASN][1000 genomes]
rs7541150	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7541309	1.00[ASN][1000 genomes]

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	nsv461628	chr1:57463326-57816489	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv546305	chr1:57463326-57816489	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv871943	chr1:57784144-57855876	Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv871530	chr1:57793948-57858319	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv817216	chr1:57801783-58130775	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv871968	chr1:57803349-57858319	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
HIV-1 control	20041166	GWAS catalog

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57792400-57806200	Weak transcription	Fetal Intestine Small	intestine
2	chr1:57800000-57826600	Weak transcription	Left Ventricle	heart
3	chr1:57802200-57809000	Weak transcription	Fetal Brain Male	brain
4	chr1:57802400-57806200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr1:57803200-57816000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:57803800-57805600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:57803800-57811600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr1:57805200-57807200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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