Variant report

Variant	rs876458
Chromosome Location	chr2:36634668-36634669
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11124512	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11673762	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs11682688	0.81[MEX][hapmap];0.83[TSI][hapmap]
rs1523788	0.84[EUR][1000 genomes]
rs17018688	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17018699	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17018723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2110928	0.84[EUR][1000 genomes]
rs2192920	0.93[EUR][1000 genomes]
rs3770883	0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3770884	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs3770887	0.86[CHB][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap]
rs3770888	0.91[CHB][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap];0.82[ASN][1000 genomes]
rs3770891	0.86[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs3770897	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3770899	0.91[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3770903	0.89[EUR][1000 genomes]
rs3770910	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3770914	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3770922	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3770926	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3770927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3770930	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3770937	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3821157	0.85[TSI][hapmap]
rs3821164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4670552	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs56036545	0.80[ASN][1000 genomes]
rs57431226	0.85[ASN][1000 genomes]
rs57785523	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs58185473	0.83[ASN][1000 genomes]
rs62136162	0.83[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	nsv833803	chr2:36589065-36745779	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv2756915	chr2:36622906-36657305	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	esv2759041	chr2:36622906-36657305	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs876458	SCARB1	trans	parietal	SCAN
rs876458	CRIM1	cis	lymphoblastoid	seeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:36604400-36640400	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr2:36604400-36640600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr2:36611600-36635400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:36616800-36635000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:36618600-36643000	Genic enhancers	Osteobl	bone
6	chr2:36620200-36635000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:36621000-36635000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr2:36621000-36635200	Weak transcription	Lung	lung
9	chr2:36621200-36634800	Weak transcription	Brain Hippocampus Middle	brain
10	chr2:36621200-36634800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr2:36621200-36635000	Weak transcription	Fetal Stomach	stomach
12	chr2:36624200-36635000	Weak transcription	Brain Angular Gyrus	brain
13	chr2:36624800-36643600	Weak transcription	Colonic Mucosa	Colon
14	chr2:36625200-36635000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr2:36625600-36635600	Weak transcription	Fetal Intestine Large	intestine
16	chr2:36625600-36643800	Weak transcription	Fetal Intestine Small	intestine
17	chr2:36625800-36642200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr2:36626000-36643800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr2:36626600-36637800	Weak transcription	Duodenum Mucosa	Duodenum
20	chr2:36629400-36635400	Weak transcription	Fetal Muscle Leg	muscle
21	chr2:36630200-36641000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr2:36630800-36635200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr2:36631000-36634800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr2:36631000-36638200	Weak transcription	Colon Smooth Muscle	Colon
25	chr2:36631000-36639000	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr2:36631000-36639600	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr2:36631200-36635200	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr2:36631400-36635000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr2:36631400-36637000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:36631400-36639000	Genic enhancers	Muscle Satellite Cultured Cells	--
31	chr2:36631400-36639000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr2:36631600-36635000	Weak transcription	HSMMtube	muscle
33	chr2:36631600-36635400	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr2:36631600-36637800	Weak transcription	Small Intestine	intestine
35	chr2:36631600-36644600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr2:36631800-36637000	Genic enhancers	HUVEC	blood vessel
37	chr2:36631800-36639600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr2:36632000-36640200	Weak transcription	Fetal Brain Female	brain
39	chr2:36632200-36648000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr2:36632400-36635600	Genic enhancers	NHEK	skin
41	chr2:36632400-36639000	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr2:36632400-36639600	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr2:36632600-36634800	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr2:36632600-36635400	Weak transcription	Fetal Muscle Trunk	muscle
45	chr2:36632600-36635400	Weak transcription	Right Atrium	heart
46	chr2:36632600-36636800	Weak transcription	Primary hematopoietic stem cells	blood
47	chr2:36632600-36638000	Weak transcription	Brain Substantia Nigra	brain
48	chr2:36632800-36635000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr2:36632800-36635000	Weak transcription	Spleen	Spleen
50	chr2:36632800-36635200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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