Variant report

Variant	rs11917431
Chromosome Location	chr3:49644012-49644013
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11130212	0.92[ASN][1000 genomes]
rs11130213	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1131095	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11709525	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11710037	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11718165	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11720597	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11919311	0.92[ASN][1000 genomes]
rs11921590	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13064576	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13085791	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13316695	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1352890	0.97[ASN][1000 genomes]
rs1873625	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1873626	0.87[ASN][1000 genomes]
rs2172252	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2329020	0.87[ASN][1000 genomes]
rs2960548	0.82[ASN][1000 genomes]
rs3197999	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34762726	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35007338	0.87[ASN][1000 genomes]
rs35404120	0.87[ASN][1000 genomes]
rs4283605	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4855847	0.87[ASN][1000 genomes]
rs4855852	0.92[ASN][1000 genomes]
rs4855881	0.82[ASN][1000 genomes]
rs6770670	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6803222	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7614725	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9812791	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9822268	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9823546	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9824092	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9827708	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9833611	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836291	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9837341	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9837520	0.89[ASN][1000 genomes]
rs9858542	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9862080	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9875617	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9882740	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	esv3324697	chr3:49641773-49644321	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
3	esv3356519	chr3:49642123-49644746	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	inside rSNPs	diseases
4	esv3371128	chr3:49642398-49644346	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11917431	FAM212A	cis	Muscle Skeletal	GTEx
rs11917431	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs11917431	IHPK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49637800-49653600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:49638000-49644600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:49638000-49647200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:49639800-49644600	Weak transcription	NHDF-Ad	bronchial
5	chr3:49640400-49646800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:49640600-49644200	Weak transcription	Hela-S3	cervix
7	chr3:49640600-49644800	Weak transcription	Brain Angular Gyrus	brain
8	chr3:49640600-49647000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:49640800-49646800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:49641000-49644600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:49641200-49644400	Weak transcription	HMEC	breast
12	chr3:49641200-49644400	Weak transcription	NHEK	skin
13	chr3:49641200-49644600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:49641200-49653600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:49643800-49644200	Enhancers	Brain Anterior Caudate	brain
16	chr3:49643800-49644600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr3:49643800-49644800	Enhancers	Spleen	Spleen
18	chr3:49643800-49645400	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr3:49643800-49645400	Enhancers	Stomach Mucosa	stomach
20	chr3:49643800-49645800	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr3:49644000-49644200	Enhancers	Pancreas	Pancrea
22	chr3:49644000-49644400	Enhancers	Lung	lung
23	chr3:49644000-49645200	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr3:49644000-49645400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:49644000-49645400	Enhancers	Brain Hippocampus Middle	brain
26	chr3:49644000-49645400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr3:49644000-49645400	Enhancers	Esophagus	oesophagus

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