Variant report

Variant	rs3856633
Chromosome Location	chr3:138005082-138005083
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs13087441	0.82[CEU][hapmap];1.00[CHB][hapmap];0.83[MEX][hapmap]
rs3732840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3773763	0.99[ASN][1000 genomes]
rs3856636	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4678406	1.00[ASW][hapmap];0.95[CEU][hapmap];0.85[CHB][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6805348	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7637162	0.86[EUR][1000 genomes]
rs7638688	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9289556	0.95[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.93[EUR][1000 genomes]
rs9846480	0.82[JPT][hapmap]
rs9846722	0.85[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs9867678	0.81[CHD][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530056	chr3:137312356-138161861	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv877537	chr3:137979007-138215114	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3856633	SR140	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:137944800-138017400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:137954600-138014400	Weak transcription	NHDF-Ad	bronchial
3	chr3:137956400-138019400	Weak transcription	Small Intestine	intestine
4	chr3:137977200-138019000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr3:137981800-138011600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:137982000-138026600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:137985200-138008200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr3:137986000-138017000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr3:137992400-138008400	Weak transcription	Stomach Mucosa	stomach
10	chr3:137992600-138005800	Weak transcription	A549	lung
11	chr3:137992600-138009000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr3:137992800-138018200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr3:137993200-138005400	Weak transcription	Esophagus	oesophagus
14	chr3:137994200-138007600	Weak transcription	Fetal Intestine Small	intestine
15	chr3:137994600-138008400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr3:137995200-138008000	Weak transcription	Hela-S3	cervix
17	chr3:137995400-138007200	Weak transcription	HUVEC	blood vessel
18	chr3:137996600-138005200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr3:137997000-138005600	Weak transcription	NH-A	brain
20	chr3:137999600-138018600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr3:137999600-138018600	Strong transcription	Adipose Nuclei	Adipose
22	chr3:137999600-138018800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr3:137999800-138018200	Strong transcription	Primary T cells from cord blood	blood
24	chr3:138000400-138017200	Strong transcription	HSMM	muscle
25	chr3:138000400-138018000	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr3:138000400-138018800	Strong transcription	Fetal Muscle Leg	muscle
27	chr3:138000400-138019000	Strong transcription	Stomach Smooth Muscle	stomach
28	chr3:138000600-138018200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr3:138000800-138018800	Strong transcription	Lung	lung
30	chr3:138001000-138016600	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr3:138001000-138018200	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr3:138001600-138010600	Strong transcription	GM12878-XiMat	blood
33	chr3:138001600-138018000	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr3:138001800-138016200	Strong transcription	Primary B cells from peripheral blood	blood
35	chr3:138001800-138017800	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr3:138001800-138017800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:138001800-138017800	Strong transcription	Liver	Liver
38	chr3:138001800-138018600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr3:138001800-138018600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr3:138001800-138018600	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr3:138002000-138006400	Strong transcription	Fetal Stomach	stomach
42	chr3:138002000-138018600	Strong transcription	Thymus	Thymus
43	chr3:138002000-138018800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr3:138002200-138018000	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr3:138002200-138018400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr3:138002200-138018600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr3:138002200-138018600	Strong transcription	Left Ventricle	heart
48	chr3:138002200-138018800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:138002400-138006000	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr3:138002400-138006200	Strong transcription	Rectal Smooth Muscle	rectum

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