Variant report

Variant	rs2538979
Chromosome Location	chr7:147582719-147582720
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10233374	0.91[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs10233755	0.81[CHB][hapmap]
rs10238572	0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs10246256	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs10952715	0.80[GIH][hapmap]
rs1177007	0.90[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs1186173	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs1861010	0.83[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1922892	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2160017	0.87[CHB][hapmap]
rs2247042	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2247043	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2247137	0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2247143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs2247149	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2373269	0.91[CHB][hapmap];0.87[YRI][hapmap]
rs2373270	0.91[CHB][hapmap];0.87[YRI][hapmap]
rs2373273	0.83[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2538972	0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2538974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2538976	0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs2538977	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2538981	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs2538983	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][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]
rs2538984	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2538985	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2538986	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2538987	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2538988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2538989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs2538990	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2538991	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2538992	0.95[CHB][hapmap];1.00[JPT][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]
rs2538994	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs2708238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2708240	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708241	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708255	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2708257	0.83[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.94[MKK][hapmap];0.87[YRI][hapmap];0.94[ASN][1000 genomes]
rs2708258	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2708270	0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2710096	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2710102	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][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]
rs2710104	0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[ASN][1000 genomes]
rs2710105	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2710107	0.83[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[MKK][hapmap];0.86[YRI][hapmap];0.94[ASN][1000 genomes]
rs2710108	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2710114	0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2710117	0.83[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2710118	0.92[ASN][1000 genomes]
rs2710120	0.96[CEU][hapmap]
rs2710121	0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs2710139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2710140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2888536	0.91[CHB][hapmap];0.87[YRI][hapmap]
rs4140925	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][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]
rs4305811	0.82[CHB][hapmap]
rs4308647	0.87[CHB][hapmap]
rs4725747	0.82[CHB][hapmap]
rs4726893	0.87[CHB][hapmap]
rs6955775	0.87[CHB][hapmap]
rs6958954	0.87[CHB][hapmap]
rs759177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs759178	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][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];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7794345	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs851712	0.89[CEU][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs851713	0.88[CEU][hapmap]
rs851715	0.95[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv465193	chr7:147512619-147583680	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
3	nsv608965	chr7:147512619-147583680	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
4	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
5	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
6	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
7	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
8	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
9	nsv889398	chr7:147569595-147588768	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	n/a
10	nsv608966	chr7:147574479-147588768	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2538979	ACTR3C	cis	parietal	SCAN
rs2538979	ATG9B	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:147582000-147584000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr7:147582000-147589400	Weak transcription	Brain Substantia Nigra	brain
3	chr7:147582200-147583200	Enhancers	Monocytes-CD14+_RO01746	blood

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