Variant report

Variant	rs9657904
Chromosome Location	chr3:105586714-105586715
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	chr17:57913805..57916301-chr3:105586626..105589272,2	MCF-7	breast:
2	chr3:105525619..105527234-chr3:105585628..105587643,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000062716	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1021858	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1021859	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1039544	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10511246	0.81[ASW][hapmap];0.93[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11921710	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11924742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12633854	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1503921	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1867192	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1867195	0.80[CEU][hapmap]
rs1910499	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2089091	0.81[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2197209	1.00[CEU][hapmap];0.83[CHB][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3996189	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs4447799	0.85[CEU][hapmap]
rs4894840	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4894957	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs57520912	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58340800	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6437620	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6437621	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6437624	0.87[CEU][hapmap]
rs6437626	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6767627	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6788366	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs6804152	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6807382	0.87[CEU][hapmap]
rs7619449	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7629357	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7634844	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7641825	0.93[CEU][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs7648842	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7649466	0.93[CEU][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7651784	0.87[CEU][hapmap]
rs9631436	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9826886	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9841500	0.87[CEU][hapmap]
rs9846534	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9869648	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9874600	1.00[CEU][hapmap];0.83[CHB][hapmap];0.97[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1008564	chr3:105554580-105643435	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1008876	chr3:105554580-105645373	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv877312	chr3:105560638-105916506	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers 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

Variant related diseases (count:1)

Disease	PMID	Source
Multiple sclerosis	20453840	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9657904	CBLB	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105563000-105586800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:105581800-105588800	Active TSS	Right Ventricle	heart
3	chr3:105582200-105588200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
4	chr3:105582200-105589000	Active TSS	Right Atrium	heart
5	chr3:105583200-105586800	Weak transcription	Spleen	Spleen
6	chr3:105583600-105589000	Active TSS	Left Ventricle	heart
7	chr3:105584200-105589200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr3:105584400-105588600	Active TSS	HSMM	muscle
9	chr3:105584600-105588600	Active TSS	Stomach Smooth Muscle	stomach
10	chr3:105584600-105589200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr3:105584800-105588600	Active TSS	NHDF-Ad	bronchial
12	chr3:105585000-105586800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr3:105585000-105587600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr3:105585000-105588400	Active TSS	Primary T cells fromperipheralblood	blood
15	chr3:105585000-105588400	Active TSS	HMEC	breast
16	chr3:105585000-105588600	Active TSS	Fetal Stomach	stomach
17	chr3:105585200-105586800	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr3:105585200-105587200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:105585200-105587400	Flanking Active TSS	Primary B cells from cord blood	blood
20	chr3:105585200-105588400	Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr3:105585200-105588400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr3:105585200-105588400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
23	chr3:105585200-105588400	Active TSS	Placenta	Placenta
24	chr3:105585200-105588400	Active TSS	NH-A	brain
25	chr3:105585200-105588600	Active TSS	Muscle Satellite Cultured Cells	--
26	chr3:105585200-105588600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:105585200-105588600	Active TSS	Fetal Muscle Leg	muscle
28	chr3:105585200-105588600	Active TSS	HSMMtube	muscle
29	chr3:105585200-105588600	Active TSS	NHLF	lung
30	chr3:105585200-105588800	Active TSS	Fetal Kidney	kidney
31	chr3:105585200-105589000	Active TSS	Ovary	ovary
32	chr3:105585200-105589000	Active TSS	Psoas Muscle	Psoas
33	chr3:105585400-105587000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr3:105585400-105587200	Flanking Active TSS	Dnd41	blood
35	chr3:105585400-105588200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
36	chr3:105585400-105588400	Active TSS	Primary T killer memory cells from peripheral blood	blood
37	chr3:105585400-105588400	Active TSS	Fetal Brain Female	brain
38	chr3:105585400-105588800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr3:105585400-105588800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr3:105585600-105586800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
41	chr3:105585600-105587200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr3:105585600-105588400	Active TSS	Fetal Lung	lung
43	chr3:105585600-105588600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr3:105585600-105588600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:105585600-105588600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr3:105585600-105588800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:105585600-105588800	Active TSS	Aorta	Aorta
48	chr3:105585600-105589000	Active TSS	Fetal Muscle Trunk	muscle
49	chr3:105585600-105589200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr3:105585800-105586800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell

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