Variant report

Variant	rs2289065
Chromosome Location	chr4:48894981-48894982
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48892295..48895717-chr4:48900323..48903334,3	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10517231	0.90[ASN][1000 genomes]
rs11727343	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs11733534	0.90[JPT][hapmap]
rs11737706	0.91[ASN][1000 genomes]
rs12504699	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12512637	0.90[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs12641022	0.83[ASN][1000 genomes]
rs13146034	0.89[ASN][1000 genomes]
rs13149083	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs1455940	0.89[ASN][1000 genomes]
rs1463365	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1463367	0.82[MEX][hapmap]
rs16861510	0.83[YRI][hapmap]
rs2085292	0.82[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs2176460	1.00[YRI][hapmap]
rs2290516	0.80[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs2354938	1.00[YRI][hapmap]
rs2572345	0.80[ASW][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs2572350	0.82[CHD][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];0.80[AFR][1000 genomes]
rs2712156	0.80[ASW][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap]
rs2712158	0.80[ASW][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs2883562	0.81[ASN][1000 genomes]
rs34730980	0.83[ASN][1000 genomes]
rs3761729	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs4694906	0.82[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs4695407	0.85[JPT][hapmap]
rs62310934	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6447670	0.90[ASN][1000 genomes]
rs724598	0.89[ASN][1000 genomes]
rs7439193	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7654032	0.85[JPT][hapmap]
rs7657332	0.93[YRI][hapmap]
rs7657698	1.00[YRI][hapmap]
rs7665209	0.87[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap]
rs7685360	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7697522	1.00[YRI][hapmap]
rs9291326	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs9997920	0.81[CHD][hapmap];0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002674	chr4:48507608-49032909	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv537087	chr4:48507608-49032909	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1010923	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv537088	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1013762	chr4:48580484-49032909	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv537089	chr4:48580484-49032909	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1010381	chr4:48701525-49309842	Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv1003718	chr4:48771947-49083089	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv916809	chr4:48784318-49083302	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv1011910	chr4:48784332-49154757	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv879010	chr4:48794403-49061141	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv1008733	chr4:48827603-48971172	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv427680	chr4:48829607-49660117	ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2289065	MGC45416	cis	multi-tissue	Pritchard
rs2289065	OCIAD2	cis	Lymphoblastoid	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48860400-48901400	Weak transcription	Brain Hippocampus Middle	brain
2	chr4:48860800-48895000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:48860800-48895000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr4:48877800-48897000	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr4:48879400-48907800	Weak transcription	Right Ventricle	heart
6	chr4:48887200-48904200	Weak transcription	Esophagus	oesophagus
7	chr4:48887800-48903800	Weak transcription	Placenta	Placenta
8	chr4:48890600-48895000	Weak transcription	HUVEC	blood vessel
9	chr4:48890600-48906200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr4:48890800-48896800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr4:48890800-48898800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:48891000-48898800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr4:48891000-48904200	Weak transcription	Spleen	Spleen
14	chr4:48891200-48898800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr4:48891200-48902000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr4:48891200-48902800	Weak transcription	Fetal Kidney	kidney
17	chr4:48891200-48907800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr4:48891200-48907800	Weak transcription	Fetal Lung	lung
19	chr4:48891400-48902000	Weak transcription	Colonic Mucosa	Colon
20	chr4:48891400-48907800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr4:48891600-48895000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr4:48891600-48895000	Weak transcription	Gastric	stomach
23	chr4:48891600-48903000	Weak transcription	Hela-S3	cervix
24	chr4:48891800-48898400	Weak transcription	Small Intestine	intestine
25	chr4:48891800-48899600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr4:48891800-48901000	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr4:48891800-48901800	Strong transcription	Fetal Thymus	thymus
28	chr4:48891800-48904600	Strong transcription	Liver	Liver
29	chr4:48892000-48895000	Weak transcription	Fetal Intestine Small	intestine
30	chr4:48892000-48895800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr4:48892000-48899400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr4:48892000-48899400	Strong transcription	Brain Germinal Matrix	brain
33	chr4:48892000-48900200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
34	chr4:48892000-48900800	Strong transcription	Primary T cells from cord blood	blood
35	chr4:48892000-48901200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr4:48892000-48901400	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr4:48892000-48901400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr4:48892000-48901400	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr4:48892000-48902000	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr4:48892000-48905400	Strong transcription	Duodenum Mucosa	Duodenum
41	chr4:48892200-48895600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr4:48892200-48896000	Strong transcription	Fetal Intestine Large	intestine
43	chr4:48892200-48900200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr4:48892200-48900600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr4:48892200-48906600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr4:48892200-48907400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr4:48892400-48897000	Weak transcription	Fetal Brain Male	brain
48	chr4:48892400-48898600	Weak transcription	Brain Anterior Caudate	brain
49	chr4:48892400-48899600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr4:48892400-48900800	Strong transcription	Primary B cells from cord blood	blood

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