Variant report

Variant	rs9837962
Chromosome Location	chr3:196287618-196287619
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:196282210..196288763-chr3:196290964..196297416,8	K562	blood:
2	chr3:196277670..196280176-chr3:196286721..196289590,3	MCF-7	breast:
3	chr3:196283678..196289168-chr3:196293009..196297108,8	MCF-7	breast:
4	chr3:196279565..196282781-chr3:196284515..196288067,4	K562	blood:

Variant related genes	Relation type
ENSG00000174013	Chromatin interaction
ENSG00000185798	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2054747	0.87[AFR][1000 genomes]
rs7374776	0.82[GIH][hapmap]
rs7616415	0.83[AFR][1000 genomes]
rs7633212	0.82[GIH][hapmap];0.80[LWK][hapmap];0.89[YRI][hapmap]
rs9819281	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003194	chr3:195960270-196342423	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv536894	chr3:195960270-196342423	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv1003066	chr3:196098763-196414159	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv948681	chr3:196148055-197007546	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	nsv1010483	chr3:196210054-196319543	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv536896	chr3:196210054-196319543	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv1014692	chr3:196242249-196531824	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	nsv878187	chr3:196245603-196554790	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
9	nsv491864	chr3:196263064-196468533	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
10	nsv829828	chr3:196268121-196463641	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9837962	TCTEX1D2	cis	cerebellum	SCAN
rs9837962	SENP5	cis	parietal	SCAN
rs9837962	OSTalpha	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196272600-196288000	Weak transcription	K562	blood
2	chr3:196276800-196293800	Weak transcription	HepG2	liver
3	chr3:196277600-196287800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr3:196277600-196290200	Weak transcription	NH-A	brain
5	chr3:196277600-196294200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr3:196277800-196287800	Weak transcription	Fetal Brain Female	brain
7	chr3:196277800-196293600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:196278000-196294400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr3:196278200-196288200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr3:196278400-196287800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:196278600-196287800	Weak transcription	Osteobl	bone
12	chr3:196278800-196287800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr3:196278800-196294600	Weak transcription	Gastric	stomach
14	chr3:196279000-196287800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr3:196279000-196289400	Weak transcription	Hela-S3	cervix
16	chr3:196279000-196294000	Weak transcription	Brain Anterior Caudate	brain
17	chr3:196279000-196294200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr3:196279200-196294000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr3:196279200-196294400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:196279400-196287800	Weak transcription	Pancreas	Pancrea
21	chr3:196279400-196294200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:196279600-196288200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:196279600-196290000	Weak transcription	Small Intestine	intestine
24	chr3:196279600-196294400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr3:196279800-196290400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr3:196279800-196294400	Weak transcription	Right Ventricle	heart
27	chr3:196279800-196294600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:196280000-196287800	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr3:196280000-196290600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr3:196280200-196294200	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr3:196280600-196289000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr3:196281400-196287800	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr3:196281600-196294600	Weak transcription	Psoas Muscle	Psoas
34	chr3:196281800-196290000	Weak transcription	HMEC	breast
35	chr3:196281800-196293600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr3:196282200-196290400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr3:196283000-196287800	Weak transcription	Fetal Intestine Small	intestine
38	chr3:196283000-196290200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr3:196283200-196289600	Weak transcription	HUVEC	blood vessel
40	chr3:196283400-196294600	Weak transcription	Fetal Brain Male	brain
41	chr3:196284400-196292600	Weak transcription	Fetal Lung	lung
42	chr3:196284600-196293800	Weak transcription	Brain Angular Gyrus	brain
43	chr3:196284600-196294600	Weak transcription	Colonic Mucosa	Colon
44	chr3:196284800-196288600	Strong transcription	Thymus	Thymus
45	chr3:196285000-196289400	Strong transcription	Fetal Muscle Trunk	muscle
46	chr3:196285000-196294400	Weak transcription	HSMM	muscle
47	chr3:196285400-196287800	Weak transcription	Esophagus	oesophagus
48	chr3:196285400-196288400	Strong transcription	Primary B cells from peripheral blood	blood
49	chr3:196285400-196290200	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr3:196285400-196294600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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