Variant report

Variant	rs10513391
Chromosome Location	chr3:150984427-150984428
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10935831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935833	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935835	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10935839	0.82[CEU][hapmap]
rs11925037	0.95[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11926145	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12107539	0.95[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12485537	0.82[EUR][1000 genomes]
rs12486265	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12497019	0.95[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12497330	0.82[CEU][hapmap]
rs12636396	0.94[CHB][hapmap];0.83[ASN][1000 genomes]
rs12637988	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12639390	0.82[CHB][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13079391	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13095610	0.82[CEU][hapmap]
rs1388617	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16863287	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[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];1.00[ASN][1000 genomes]
rs1882013	0.82[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.88[MKK][hapmap];0.82[ASN][1000 genomes]
rs2307020	0.82[CEU][hapmap]
rs28527299	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34347156	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34708786	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34997694	0.93[AFR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35144003	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35786948	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3732759	0.82[CEU][hapmap]
rs3773621	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3806636	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4680256	0.82[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4680262	0.81[ASN][1000 genomes]
rs4680263	1.00[CHD][hapmap];0.85[GIH][hapmap];0.83[MKK][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs4680307	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4680315	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4680356	0.95[CEU][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55705054	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56087525	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58139829	0.94[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs62282985	0.82[ASN][1000 genomes]
rs62282988	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62283022	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6440738	0.82[CEU][hapmap]
rs66524723	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66927386	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6767192	0.82[CEU][hapmap]
rs6784934	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6785930	0.95[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6790448	0.82[CEU][hapmap]
rs6793898	0.82[CEU][hapmap]
rs6796501	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6801155	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6801273	0.82[CEU][hapmap]
rs6804769	0.82[CEU][hapmap]
rs6808091	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7428575	0.82[CEU][hapmap]
rs7618206	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7620767	0.88[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7644001	0.82[CEU][hapmap]
rs7648875	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460894	chr3:150770614-151095093	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv592045	chr3:150770614-151095093	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2754555	chr3:150968302-151054302	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10513391	FAM194A	cis	parietal	SCAN
rs10513391	MED12L	cis	cerebellum	SCAN
rs10513391	CLRN1	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150974400-150987600	Weak transcription	Aorta	Aorta
2	chr3:150977800-151000000	Weak transcription	Placenta	Placenta
3	chr3:150979400-150987600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr3:150981400-150984600	Enhancers	Fetal Stomach	stomach
5	chr3:150981400-150986800	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr3:150981600-150986800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr3:150981800-150986400	Enhancers	Rectal Smooth Muscle	rectum
8	chr3:150981800-150994000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr3:150982000-150984800	Enhancers	Brain Anterior Caudate	brain
10	chr3:150982000-150985200	Enhancers	Primary hematopoietic stem cells	blood
11	chr3:150982400-150984800	Enhancers	Primary B cells from peripheral blood	blood
12	chr3:150982400-150985000	Enhancers	Stomach Smooth Muscle	stomach
13	chr3:150982600-150984600	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr3:150982600-150984600	Enhancers	Fetal Muscle Leg	muscle
15	chr3:150982800-150984800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:150982800-150986200	Weak transcription	Stomach Mucosa	stomach
17	chr3:150983000-151011000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:150983400-150984600	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr3:150983400-150984600	Enhancers	GM12878-XiMat	blood
20	chr3:150983400-150984800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr3:150983600-150984600	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr3:150983600-150984600	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr3:150983600-150984800	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr3:150983600-150987600	Weak transcription	Brain Hippocampus Middle	brain
25	chr3:150983800-150984600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:150983800-150984800	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr3:150983800-150984800	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr3:150983800-150985400	Enhancers	Fetal Lung	lung
29	chr3:150983800-150986400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr3:150983800-150986400	Weak transcription	Adipose Nuclei	Adipose
31	chr3:150983800-150989400	Enhancers	Primary B cells from cord blood	blood
32	chr3:150983800-151000600	Weak transcription	Brain Substantia Nigra	brain
33	chr3:150984000-150984600	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr3:150984000-150984600	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr3:150984000-150986800	Weak transcription	Fetal Thymus	thymus
36	chr3:150984000-150996000	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr3:150984200-150984600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr3:150984200-150984800	Enhancers	Monocytes-CD14+_RO01746	blood
39	chr3:150984200-150998800	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr3:150984400-150984600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:150984400-150984600	Flanking Active TSS	Colon Smooth Muscle	Colon
42	chr3:150984400-150984600	Enhancers	Duodenum Mucosa	Duodenum
43	chr3:150984400-150984800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr3:150984400-151022400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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