Variant report

Variant	rs17197782
Chromosome Location	chr7:150522100-150522101
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10378	0.91[CEU][hapmap];0.82[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1547958	1.00[JPT][hapmap]
rs1805123	1.00[JPT][hapmap]
rs28360734	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28508254	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28592021	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2907948	1.00[JPT][hapmap]
rs2968854	1.00[JPT][hapmap]
rs2968856	1.00[JPT][hapmap]
rs2968863	1.00[JPT][hapmap]
rs2968864	1.00[JPT][hapmap]
rs3918227	1.00[LWK][hapmap]
rs57543564	0.86[ASN][1000 genomes]
rs62490434	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62490441	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62492366	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs714883	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs877120	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]

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	nsv608990	chr7:149961274-150707488	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv1017368	chr7:150016952-150655773	Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
3	nsv539195	chr7:150016952-150655773	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv1030109	chr7:150312916-150701010	Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv967475	chr7:150323577-150610034	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17197782	ZNF862	cis	cerebellum	SCAN
rs17197782	CNTNAP2	cis	parietal	SCAN
rs17197782	TDRD1	trans	lymphoblastoid	seeQTL
rs17197782	TMEM176A	cis	lymphoblastoid	seeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150503400-150528000	Weak transcription	Ovary	ovary
2	chr7:150512000-150522800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr7:150518400-150523200	Weak transcription	Right Atrium	heart
4	chr7:150518600-150522400	Weak transcription	Fetal Intestine Small	intestine
5	chr7:150519800-150523400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr7:150519800-150525200	Enhancers	Fetal Heart	heart
7	chr7:150520200-150523600	Enhancers	Placenta	Placenta
8	chr7:150520800-150522800	Enhancers	Liver	Liver
9	chr7:150521200-150522400	Weak transcription	Duodenum Mucosa	Duodenum
10	chr7:150521600-150522400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr7:150521800-150523200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr7:150522000-150522200	Enhancers	Stomach Smooth Muscle	stomach
13	chr7:150522000-150522400	ZNF genes & repeats	Fetal Stomach	stomach
14	chr7:150522000-150523400	Enhancers	Right Ventricle	heart
15	chr7:150522000-150523800	Enhancers	Left Ventricle	heart

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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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