Variant report

Variant	rs12756748
Chromosome Location	chr1:179757855-179757856
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10913889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125387	1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125434	1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12130143	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133344	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12134289	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12723969	0.83[CEU][hapmap]
rs12756362	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs17370139	0.83[CEU][hapmap]
rs34233788	0.82[EUR][1000 genomes]
rs71630240	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009961	chr1:179714247-179790110	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1011407	chr1:179733193-179799430	Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12756748	FAM163A	cis	parietal	SCAN
rs12756748	IER5	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179753200-179758200	Enhancers	Duodenum Mucosa	Duodenum
2	chr1:179754000-179758000	Enhancers	Brain Germinal Matrix	brain
3	chr1:179756000-179758200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:179756200-179758200	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr1:179756600-179758000	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr1:179756600-179758200	Enhancers	H1 Cell Line	embryonic stem cell
7	chr1:179756600-179758400	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr1:179756800-179758200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:179756800-179758200	Enhancers	Fetal Intestine Small	intestine
10	chr1:179757000-179758000	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr1:179757000-179758200	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr1:179757000-179758200	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr1:179757000-179758200	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr1:179757000-179758400	Enhancers	Fetal Intestine Large	intestine
15	chr1:179757600-179758200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr1:179757600-179758200	Enhancers	H9 Cell Line	embryonic stem cell
17	chr1:179757600-179758200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:179757800-179764400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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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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