Variant report

Variant	rs10877185
Chromosome Location	chr12:59297986-59297987
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1020031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877182	1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs10877183	1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs10877184	0.81[YRI][hapmap]
rs10877186	0.81[YRI][hapmap]
rs11172790	0.83[TSI][hapmap]
rs11172795	0.81[EUR][1000 genomes]
rs11172797	0.86[EUR][1000 genomes]
rs11172801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172802	0.92[EUR][1000 genomes]
rs11172804	0.92[EUR][1000 genomes]
rs11172805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172806	0.89[EUR][1000 genomes]
rs11172807	0.92[EUR][1000 genomes]
rs11172808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172809	0.92[EUR][1000 genomes]
rs11172811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172812	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172816	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11172817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172818	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12146851	0.89[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs13377741	0.81[ASW][hapmap];1.00[MEX][hapmap]
rs17120227	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17617428	0.81[EUR][1000 genomes]
rs2167030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2279718	0.83[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758311	chr12:59022729-59323045	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv2759902	chr12:59022729-59323045	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv1043385	chr12:59149582-59758952	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1067596	chr12:59167152-59764208	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv492251	chr12:59167152-59764208	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10877185	SLC47A2	trans	brain	seeQTL
rs10877185	CAPS	trans	brain	seeQTL
rs10877185	TRAK2	trans	brain	seeQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59266000-59311000	Weak transcription	Fetal Thymus	thymus
2	chr12:59275000-59300800	Weak transcription	HSMMtube	muscle
3	chr12:59279000-59310800	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr12:59279200-59309400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr12:59283400-59298000	Weak transcription	Fetal Brain Male	brain
6	chr12:59283800-59300400	Weak transcription	Placenta	Placenta
7	chr12:59284000-59298000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr12:59284000-59298000	Weak transcription	HSMM	muscle
9	chr12:59284000-59300800	Weak transcription	Colonic Mucosa	Colon
10	chr12:59284000-59300800	Weak transcription	HepG2	liver
11	chr12:59284200-59304600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr12:59284600-59298000	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr12:59286800-59298000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr12:59287800-59298000	Weak transcription	Brain Angular Gyrus	brain
15	chr12:59287800-59301800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr12:59288200-59298000	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr12:59288200-59298600	Weak transcription	NHLF	lung
18	chr12:59289200-59298000	Weak transcription	HUVEC	blood vessel
19	chr12:59289200-59300800	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr12:59289400-59301200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr12:59289600-59300800	Weak transcription	Aorta	Aorta
22	chr12:59289800-59298000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr12:59289800-59300800	Weak transcription	Lung	lung
24	chr12:59289800-59304600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr12:59289800-59305400	Weak transcription	Spleen	Spleen
26	chr12:59290600-59298000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr12:59290600-59300800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr12:59290600-59300800	Weak transcription	Brain Hippocampus Middle	brain
29	chr12:59290600-59307200	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr12:59290600-59311000	Weak transcription	Right Ventricle	heart
31	chr12:59291200-59298000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr12:59291800-59302800	Weak transcription	Psoas Muscle	Psoas
33	chr12:59292000-59298400	Weak transcription	Colon Smooth Muscle	Colon
34	chr12:59292000-59300800	Weak transcription	Brain Cingulate Gyrus	brain
35	chr12:59292200-59300800	Weak transcription	Brain Substantia Nigra	brain
36	chr12:59292400-59298000	Weak transcription	Left Ventricle	heart
37	chr12:59292400-59309200	Weak transcription	Fetal Heart	heart
38	chr12:59292400-59310600	Weak transcription	Small Intestine	intestine
39	chr12:59292600-59301600	Weak transcription	Gastric	stomach
40	chr12:59292600-59303000	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr12:59293000-59298000	Weak transcription	Ovary	ovary
42	chr12:59293000-59298000	Weak transcription	Stomach Mucosa	stomach
43	chr12:59293000-59301200	Weak transcription	Esophagus	oesophagus
44	chr12:59293600-59300800	Weak transcription	Pancreas	Pancrea
45	chr12:59294200-59298000	Weak transcription	Stomach Smooth Muscle	stomach
46	chr12:59295400-59302800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr12:59295600-59298000	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr12:59296200-59298000	Weak transcription	NHEK	skin
49	chr12:59296200-59299600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr12:59297800-59298000	Strong transcription	Skeletal Muscle Female	skeletal muscle

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