Variant report

Variant	rs2470954
Chromosome Location	chr7:104448511-104448512
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10227192	0.84[EUR][1000 genomes]
rs10953451	0.95[CEU][hapmap];0.82[JPT][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs11771722	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs12670336	0.81[CEU][hapmap]
rs12672558	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs17141483	0.81[CEU][hapmap]
rs17141520	0.81[CEU][hapmap]
rs2470955	0.84[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2470957	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470958	0.95[EUR][1000 genomes]
rs2470959	1.00[CEU][hapmap];0.87[GIH][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs2470964	0.90[CEU][hapmap];0.82[JPT][hapmap];0.98[EUR][1000 genomes]
rs2470965	0.95[CEU][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes]
rs2470966	0.94[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs4582489	0.96[EUR][1000 genomes]

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	nsv429790	chr7:104314049-104488049	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv429792	chr7:104400049-104488049	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv5887	chr7:104401250-104491604	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1030875	chr7:104409391-104472647	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1028479	chr7:104409391-104479087	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv528392	chr7:104411273-104466675	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv522743	chr7:104411273-104486707	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv831086	chr7:104422503-104596766	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv1019625	chr7:104429371-104461487	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2470954	ARMC10	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:104440400-104482400	Weak transcription	Fetal Intestine Small	intestine
2	chr7:104444400-104449000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr7:104444600-104450000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr7:104446600-104455200	Weak transcription	Brain Hippocampus Middle	brain
5	chr7:104448000-104448800	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr7:104448200-104448600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr7:104448200-104448600	Enhancers	Brain Substantia Nigra	brain
8	chr7:104448400-104448600	Enhancers	Brain Cingulate Gyrus	brain

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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