Variant report

Variant	rs9846722
Chromosome Location	chr3:137997835-137997836
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs13087441	0.85[CHB][hapmap]
rs2291093	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs3732840	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3773763	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3856633	0.85[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs3856636	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4678406	1.00[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs6778511	0.84[CHD][hapmap]
rs6805348	0.85[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs7612622	0.81[CHD][hapmap]
rs7638688	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs9289556	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9846480	0.90[JPT][hapmap]
rs9867678	0.90[JPT][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9846722	SR140	cis	parietal	SCAN
rs9846722	ESYT3	cis	cerebellum	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	chr3:137964800-138003800	Weak transcription	K562	blood
5	chr3:137971800-138001600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:137977200-138019000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr3:137978200-138000800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:137981800-138011600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:137982000-138026600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr3:137985200-138008200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:137986000-138017000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr3:137991000-138003000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr3:137992200-138003800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr3:137992400-138000800	Weak transcription	Lung	lung
15	chr3:137992400-138008400	Weak transcription	Stomach Mucosa	stomach
16	chr3:137992600-138002400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:137992600-138002800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr3:137992600-138002800	Weak transcription	Colonic Mucosa	Colon
19	chr3:137992600-138003200	Weak transcription	NHLF	lung
20	chr3:137992600-138003600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr3:137992600-138003600	Weak transcription	Psoas Muscle	Psoas
22	chr3:137992600-138004200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr3:137992600-138004400	Weak transcription	Pancreas	Pancrea
24	chr3:137992600-138005800	Weak transcription	A549	lung
25	chr3:137992600-138009000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr3:137992800-138000200	Weak transcription	HMEC	breast
27	chr3:137992800-138002600	Weak transcription	Right Ventricle	heart
28	chr3:137992800-138003400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:137992800-138018200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr3:137993000-138002400	Weak transcription	Gastric	stomach
31	chr3:137993000-138002600	Weak transcription	Aorta	Aorta
32	chr3:137993000-138003600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr3:137993000-138003800	Weak transcription	Brain Angular Gyrus	brain
34	chr3:137993200-138005400	Weak transcription	Esophagus	oesophagus
35	chr3:137993600-138003200	Weak transcription	Brain Germinal Matrix	brain
36	chr3:137993800-137999600	Weak transcription	Fetal Stomach	stomach
37	chr3:137993800-137999800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr3:137993800-138000600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr3:137993800-138002600	Weak transcription	HepG2	liver
40	chr3:137993800-138003000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr3:137993800-138003200	Weak transcription	Fetal Kidney	kidney
42	chr3:137993800-138003200	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr3:137993800-138003200	Weak transcription	Spleen	Spleen
44	chr3:137993800-138003400	Weak transcription	Osteobl	bone
45	chr3:137993800-138003600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr3:137993800-138005000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr3:137994000-137999800	Weak transcription	Fetal Muscle Trunk	muscle
48	chr3:137994000-138001600	Weak transcription	GM12878-XiMat	blood
49	chr3:137994000-138002000	Weak transcription	Thymus	Thymus
50	chr3:137994000-138002400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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