Variant report

Variant	rs7638504
Chromosome Location	chr3:105499373-105499374
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	chr3:105497500..105500139-chr3:105500274..105501917,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11919893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11926659	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486371	0.83[CEU][hapmap]
rs12496588	0.83[CEU][hapmap]
rs12497428	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12632980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13090949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13326550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13433776	1.00[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1503923	0.81[ASN][1000 genomes]
rs16851596	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16851705	0.84[ASN][1000 genomes]
rs16851706	0.83[ASN][1000 genomes]
rs2120103	0.90[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs2120104	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2399056	0.92[CEU][hapmap]
rs6437616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6766168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6776593	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6778745	0.83[CEU][hapmap]
rs6780432	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6791765	0.83[CEU][hapmap]
rs7634195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7639888	0.83[CEU][hapmap]
rs894541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9811776	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9814582	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9837243	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9838755	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9846445	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9849559	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9859953	0.87[ASW][hapmap]
rs9872895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9876110	0.83[CEU][hapmap]
rs9880744	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877309	chr3:105373836-105542435	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	esv2755185	chr3:105378310-105597310	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv591246	chr3:105439522-105504129	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7638504	CBLB	cis	cerebellum	SCAN
rs7638504	GUCA1C	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105467600-105509400	Weak transcription	Stomach Mucosa	stomach
2	chr3:105472400-105504400	Weak transcription	HUVEC	blood vessel
3	chr3:105478600-105509400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr3:105478600-105511200	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr3:105481200-105500800	Weak transcription	Small Intestine	intestine
6	chr3:105481400-105509600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr3:105481800-105507400	Weak transcription	HSMM	muscle
8	chr3:105482000-105503800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:105482000-105509200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr3:105482000-105509600	Weak transcription	Ovary	ovary
11	chr3:105482000-105510800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:105482000-105511200	Weak transcription	Aorta	Aorta
13	chr3:105482400-105500000	Weak transcription	Fetal Stomach	stomach
14	chr3:105482800-105517400	Weak transcription	Fetal Intestine Large	intestine
15	chr3:105483200-105506200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:105483200-105555200	Weak transcription	Placenta	Placenta
17	chr3:105486800-105519000	Weak transcription	Esophagus	oesophagus
18	chr3:105487000-105508400	Weak transcription	Fetal Lung	lung
19	chr3:105487200-105508400	Weak transcription	Fetal Kidney	kidney
20	chr3:105487400-105500600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr3:105487400-105504200	Weak transcription	Fetal Heart	heart
22	chr3:105489400-105506000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr3:105489600-105509600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr3:105489600-105525400	Weak transcription	Fetal Intestine Small	intestine
25	chr3:105493000-105501400	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr3:105493000-105501400	Weak transcription	Left Ventricle	heart
27	chr3:105493000-105502400	Weak transcription	Brain Anterior Caudate	brain
28	chr3:105493000-105511200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr3:105493000-105511200	Weak transcription	Right Atrium	heart
30	chr3:105493200-105501400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr3:105493200-105509000	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr3:105494000-105506200	Weak transcription	Primary hematopoietic stem cells	blood
33	chr3:105494400-105509400	Weak transcription	Primary B cells from cord blood	blood
34	chr3:105494400-105516200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr3:105494800-105500000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr3:105494800-105500800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr3:105495000-105500800	Weak transcription	Primary T cells from cord blood	blood
38	chr3:105495000-105509600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr3:105495200-105500000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr3:105495200-105500800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr3:105495400-105517200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr3:105495600-105503800	Weak transcription	GM12878-XiMat	blood
43	chr3:105495600-105504600	Weak transcription	Osteobl	bone
44	chr3:105495600-105509400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr3:105496200-105506000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr3:105496400-105510800	Weak transcription	Right Ventricle	heart
47	chr3:105496400-105514000	Weak transcription	Lung	lung
48	chr3:105496600-105500800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr3:105497000-105500600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr3:105497000-105500600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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