Variant report

Variant	rs3770922
Chromosome Location	chr2:36632040-36632041
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11124512	0.88[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11673762	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs11682688	0.81[MEX][hapmap];0.83[TSI][hapmap]
rs1523788	0.83[EUR][1000 genomes]
rs17018688	1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17018699	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17018723	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2110928	0.83[EUR][1000 genomes]
rs2192920	0.92[EUR][1000 genomes]
rs3770883	0.91[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes]
rs3770884	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs3770887	0.86[CHB][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap]
rs3770888	0.91[CHB][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap]
rs3770891	0.86[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs3770897	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3770899	0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3770903	0.88[EUR][1000 genomes]
rs3770910	0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3770914	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3770926	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3770927	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3770930	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3770937	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3821157	0.85[TSI][hapmap]
rs3821164	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4670552	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs57431226	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs57785523	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs58185473	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs62136162	0.81[AMR][1000 genomes]
rs876458	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]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3770922	SCARB1	trans	parietal	SCAN

Chromatin state (count:94 , 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	chr2:36611600-36632400	Weak transcription	Esophagus	oesophagus
4	chr2:36611600-36635400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:36616800-36635000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr2:36617000-36633400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr2:36617200-36633800	Weak transcription	Fetal Lung	lung
8	chr2:36618600-36643000	Genic enhancers	Osteobl	bone
9	chr2:36620200-36635000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:36621000-36635000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr2:36621000-36635200	Weak transcription	Lung	lung
12	chr2:36621200-36634800	Weak transcription	Brain Hippocampus Middle	brain
13	chr2:36621200-36634800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr2:36621200-36635000	Weak transcription	Fetal Stomach	stomach
15	chr2:36623000-36632200	Weak transcription	Right Atrium	heart
16	chr2:36624200-36635000	Weak transcription	Brain Angular Gyrus	brain
17	chr2:36624600-36634600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr2:36624800-36643600	Weak transcription	Colonic Mucosa	Colon
19	chr2:36625200-36635000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr2:36625600-36635600	Weak transcription	Fetal Intestine Large	intestine
21	chr2:36625600-36643800	Weak transcription	Fetal Intestine Small	intestine
22	chr2:36625800-36642200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr2:36626000-36643800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr2:36626400-36632400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr2:36626600-36632400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr2:36626600-36637800	Weak transcription	Duodenum Mucosa	Duodenum
27	chr2:36627200-36634000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr2:36627800-36634600	Weak transcription	Fetal Heart	heart
29	chr2:36628000-36632200	Weak transcription	Brain Germinal Matrix	brain
30	chr2:36628600-36634200	Enhancers	NHDF-Ad	bronchial
31	chr2:36629000-36632800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr2:36629200-36632400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr2:36629200-36632400	Weak transcription	Left Ventricle	heart
34	chr2:36629200-36633400	Weak transcription	Ovary	ovary
35	chr2:36629400-36635400	Weak transcription	Fetal Muscle Leg	muscle
36	chr2:36630000-36632800	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr2:36630200-36632800	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr2:36630200-36633000	Enhancers	Aorta	Aorta
39	chr2:36630200-36641000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr2:36630600-36632600	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr2:36630600-36633200	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr2:36630800-36632200	Enhancers	Rectal Smooth Muscle	rectum
43	chr2:36630800-36633400	Enhancers	NHLF	lung
44	chr2:36630800-36635200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr2:36631000-36632400	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr2:36631000-36632600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr2:36631000-36632800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
48	chr2:36631000-36632800	Enhancers	Primary B cells from peripheral blood	blood
49	chr2:36631000-36634800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:36631000-36638200	Weak transcription	Colon Smooth Muscle	Colon

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