Variant report

Variant	rs7374776
Chromosome Location	chr3:196282086-196282087
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:196281289..196284000-chr3:196298960..196301880,2	MCF-7	breast:
2	chr3:196273664..196275674-chr3:196279813..196283038,3	K562	blood:
3	chr3:196279565..196282781-chr3:196284515..196288067,4	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11185547	0.83[GIH][hapmap]
rs2054747	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6583312	1.00[ASN][1000 genomes]
rs6583314	1.00[ASN][1000 genomes]
rs6583315	1.00[ASN][1000 genomes]
rs6767712	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6768682	1.00[ASN][1000 genomes]
rs6783108	1.00[ASN][1000 genomes]
rs6786154	1.00[ASN][1000 genomes]
rs6807731	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615630	1.00[ASN][1000 genomes]
rs7616415	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7623203	1.00[ASN][1000 genomes]
rs7625068	1.00[ASN][1000 genomes]
rs7633212	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7640505	0.84[ASN][1000 genomes]
rs9819281	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9837962	0.82[GIH][hapmap]
rs9850782	0.94[CEU][hapmap];0.99[EUR][1000 genomes]
rs9866935	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	esv2752687	chr3:196147690-196286690	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	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
10	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
11	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7374776	OSTalpha	cis	cerebellum	SCAN
rs7374776	MGC33212	cis	multi-tissue	Pritchard

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196272600-196287400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:196272600-196288000	Weak transcription	K562	blood
3	chr3:196274200-196286800	Weak transcription	Liver	Liver
4	chr3:196276800-196293800	Weak transcription	HepG2	liver
5	chr3:196277000-196285800	Weak transcription	Fetal Muscle Leg	muscle
6	chr3:196277400-196285400	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr3:196277600-196284800	Weak transcription	Thymus	Thymus
8	chr3:196277600-196287800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:196277600-196290200	Weak transcription	NH-A	brain
10	chr3:196277600-196294200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr3:196277800-196285800	Weak transcription	Aorta	Aorta
12	chr3:196277800-196287600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:196277800-196287600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr3:196277800-196287800	Weak transcription	Fetal Brain Female	brain
15	chr3:196277800-196293600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:196278000-196286000	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr3:196278000-196286400	Weak transcription	Fetal Stomach	stomach
18	chr3:196278000-196287600	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr3:196278000-196287600	Weak transcription	HSMMtube	muscle
20	chr3:196278000-196294400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr3:196278200-196287400	Weak transcription	NHDF-Ad	bronchial
22	chr3:196278200-196288200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr3:196278400-196287800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr3:196278600-196285000	Weak transcription	Fetal Muscle Trunk	muscle
25	chr3:196278600-196286600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:196278600-196287800	Weak transcription	Osteobl	bone
27	chr3:196278800-196285800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr3:196278800-196287800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr3:196278800-196294600	Weak transcription	Gastric	stomach
30	chr3:196279000-196286600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:196279000-196287400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:196279000-196287400	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr3:196279000-196287800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr3:196279000-196289400	Weak transcription	Hela-S3	cervix
35	chr3:196279000-196294000	Weak transcription	Brain Anterior Caudate	brain
36	chr3:196279000-196294200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr3:196279200-196285000	Weak transcription	Placenta	Placenta
38	chr3:196279200-196285600	Weak transcription	Colon Smooth Muscle	Colon
39	chr3:196279200-196286000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:196279200-196286200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:196279200-196286400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr3:196279200-196286800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr3:196279200-196294000	Weak transcription	Brain Cingulate Gyrus	brain
44	chr3:196279200-196294400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr3:196279400-196286200	Weak transcription	Ovary	ovary
46	chr3:196279400-196287800	Weak transcription	Pancreas	Pancrea
47	chr3:196279400-196294200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr3:196279600-196285000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr3:196279600-196286000	Weak transcription	Fetal Kidney	kidney
50	chr3:196279600-196286200	Weak transcription	Stomach Smooth Muscle	stomach

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