Variant report

Variant	rs1332622
Chromosome Location	chr10:45420076-45420077
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10900131	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11239278	1.00[CEU][hapmap];0.95[CHB][hapmap];0.80[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11239282	0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs17417442	0.80[CHD][hapmap]
rs2065465	1.00[CEU][hapmap];0.95[GIH][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4543933	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6593448	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7077388	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7082940	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7085840	1.00[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];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7095112	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs7098274	1.00[CEU][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7477198	0.81[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap]
rs7911339	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs932986	1.00[CEU][hapmap];0.95[CHB][hapmap];0.80[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831845	chr10:45300268-45460395	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv831846	chr10:45322236-45556370	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv466909	chr10:45408011-45446791	Enhancers Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv550714	chr10:45408011-45446791	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv3374788	chr10:45419346-45423644	Genic enhancers Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv818757	chr10:45420076-45431321	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1332622	RASGEF1A	cis	cerebellum	SCAN
rs1332622	ZNF488	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:45407800-45422800	Weak transcription	Ovary	ovary
2	chr10:45410200-45430400	Weak transcription	Gastric	stomach
3	chr10:45413200-45420400	Weak transcription	Fetal Kidney	kidney
4	chr10:45413400-45428200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr10:45417000-45434000	Weak transcription	Fetal Brain Female	brain
6	chr10:45417800-45422400	Weak transcription	Duodenum Mucosa	Duodenum
7	chr10:45418800-45420800	Weak transcription	Spleen	Spleen
8	chr10:45418800-45424800	Weak transcription	Colonic Mucosa	Colon
9	chr10:45419200-45420200	Weak transcription	Lung	lung
10	chr10:45419200-45420200	Weak transcription	Pancreas	Pancrea
11	chr10:45419400-45420800	Enhancers	Fetal Thymus	thymus
12	chr10:45419600-45420400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr10:45419600-45421000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr10:45419800-45420600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr10:45419800-45421000	Enhancers	Fetal Muscle Trunk	muscle
16	chr10:45419800-45421200	Enhancers	Fetal Muscle Leg	muscle
17	chr10:45420000-45420200	Bivalent Enhancer	HepG2	liver
18	chr10:45420000-45420400	Enhancers	H1 Cell Line	embryonic stem cell
19	chr10:45420000-45421200	Enhancers	HSMMtube	muscle

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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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