Variant report

Variant	rs12495561
Chromosome Location	chr3:51275257-51275258
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs12485331	0.84[EUR][1000 genomes]
rs12485754	0.84[EUR][1000 genomes]
rs12487468	0.82[CHB][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs12487496	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12489219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12490026	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12491836	0.89[EUR][1000 genomes]
rs12492615	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[EUR][1000 genomes]
rs12492690	0.89[EUR][1000 genomes]
rs12493034	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12493323	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12493978	0.82[CHB][hapmap];0.82[AMR][1000 genomes]
rs12496830	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1480366	0.81[YRI][hapmap]
rs17051685	0.90[YRI][hapmap]
rs1809388	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1842394	0.89[CHB][hapmap];0.88[AMR][1000 genomes]
rs2086395	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2101056	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2127654	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2170177	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2306430	0.84[CHB][hapmap]
rs2306431	0.82[CHB][hapmap]
rs2355946	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3762711	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3828395	0.82[CHB][hapmap]
rs4130473	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[EUR][1000 genomes]
rs4346580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs4468966	0.82[CHB][hapmap];0.83[AMR][1000 genomes]
rs4927961	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs4974096	0.82[CHB][hapmap]
rs4974100	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4974112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56052360	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57406588	0.89[EUR][1000 genomes]
rs58201844	0.83[AMR][1000 genomes]
rs58911602	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59129045	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59682667	0.89[EUR][1000 genomes]
rs59834534	0.89[EUR][1000 genomes]
rs60128296	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60461297	0.89[EUR][1000 genomes]
rs60567238	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60740654	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61578076	0.81[AFR][1000 genomes]
rs61660900	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6792254	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72936442	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72936462	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72941919	0.89[EUR][1000 genomes]
rs72943166	0.89[EUR][1000 genomes]
rs72948197	0.89[EUR][1000 genomes]
rs72948200	0.89[EUR][1000 genomes]
rs72953143	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72953162	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72953175	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs751076	0.84[AMR][1000 genomes]
rs880477	0.90[YRI][hapmap]
rs880478	0.84[CHB][hapmap];0.84[AMR][1000 genomes]
rs9817077	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[AMR][1000 genomes]
rs9817872	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[AMR][1000 genomes]
rs9819195	0.82[CHB][hapmap];0.83[AMR][1000 genomes]
rs9829057	0.82[CHB][hapmap];0.83[AMR][1000 genomes]
rs9856134	0.82[CHB][hapmap];0.83[AMR][1000 genomes]
rs9878592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1005858	chr3:51090373-51444027	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv536569	chr3:51090373-51444027	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12495561	HEMK	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51235800-51285000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:51248000-51282600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:51252000-51288200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:51252000-51312600	Weak transcription	HSMMtube	muscle
5	chr3:51252800-51277000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:51253400-51312200	Weak transcription	Brain Substantia Nigra	brain
7	chr3:51255000-51276200	Weak transcription	Fetal Brain Male	brain
8	chr3:51257400-51279600	Weak transcription	Brain Anterior Caudate	brain
9	chr3:51259800-51284000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:51259800-51284000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr3:51260000-51284400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr3:51260000-51284800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:51265800-51284000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr3:51266400-51276200	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr3:51266400-51284200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:51266400-51284200	Weak transcription	Brain Angular Gyrus	brain
17	chr3:51266400-51284800	Weak transcription	Brain Germinal Matrix	brain
18	chr3:51266400-51297000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:51267000-51297600	Weak transcription	Stomach Smooth Muscle	stomach
20	chr3:51267200-51277200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr3:51267600-51279400	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr3:51267800-51277600	Weak transcription	Fetal Brain Female	brain
23	chr3:51268000-51296200	Weak transcription	Brain Hippocampus Middle	brain
24	chr3:51274000-51275400	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr3:51274800-51276600	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr3:51274800-51284000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr3:51275000-51280000	Weak transcription	Brain Cingulate Gyrus	brain

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