Variant report

Variant	rs2538976
Chromosome Location	chr7:147585819-147585820
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10270089	0.84[ASN][1000 genomes]
rs10952715	0.80[GIH][hapmap]
rs11980029	0.86[LWK][hapmap]
rs1922892	0.93[EUR][1000 genomes]
rs2215798	0.86[LWK][hapmap]
rs2247042	0.94[EUR][1000 genomes]
rs2247043	0.94[EUR][1000 genomes]
rs2247137	0.94[EUR][1000 genomes]
rs2247143	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs2247149	0.94[EUR][1000 genomes]
rs2538974	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs2538975	0.89[LWK][hapmap]
rs2538977	0.94[EUR][1000 genomes]
rs2538979	0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs2538981	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2538983	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs2538984	0.93[EUR][1000 genomes]
rs2538985	0.94[EUR][1000 genomes]
rs2538986	0.94[EUR][1000 genomes]
rs2538987	0.94[EUR][1000 genomes]
rs2538988	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs2538989	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs2538990	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs2538991	0.94[EUR][1000 genomes]
rs2538992	0.94[EUR][1000 genomes]
rs2708238	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs2708239	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs2708240	0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs2708241	0.94[EUR][1000 genomes]
rs2708243	0.95[CEU][hapmap];0.94[EUR][1000 genomes]
rs2708244	0.86[LWK][hapmap]
rs2708255	0.94[EUR][1000 genomes]
rs2708269	0.87[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs2710096	0.93[EUR][1000 genomes]
rs2710102	0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs2710105	0.96[CEU][hapmap]
rs2710108	0.96[CEU][hapmap]
rs2710109	0.84[LWK][hapmap]
rs2710119	0.84[ASN][1000 genomes]
rs2710120	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs2710139	0.96[CEU][hapmap]
rs2710140	0.96[CEU][hapmap]
rs4140925	0.95[CEU][hapmap];0.94[EUR][1000 genomes]
rs759177	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs759178	0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs7794345	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs851712	0.85[CEU][hapmap];0.83[TSI][hapmap]
rs851713	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv889397	chr7:147471710-147585819	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
2	nsv1023913	chr7:147521075-147806318	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1026058	chr7:147521109-147783042	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv539179	chr7:147521109-147783042	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv934002	chr7:147521110-147807705	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1017610	chr7:147523752-147806427	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv889398	chr7:147569595-147588768	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	n/a
8	nsv608966	chr7:147574479-147588768	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	inside rSNPs	n/a
9	esv3441359	chr7:147585772-147592059	Enhancers Weak transcription	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2538976	ATG9B	cis	parietal	SCAN
rs2538976	ACTR3C	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:147582000-147589400	Weak transcription	Brain Substantia Nigra	brain

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