Variant report

Variant	rs6490103
Chromosome Location	chr12:117442636-117442637
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:117441591..117444664-chr12:117447106..117450120,5	MCF-7	breast:
2	chr12:117437746..117440229-chr12:117441303..117443639,2	K562	blood:
3	chr12:117442448..117444268-chr12:117445719..117447453,2	K562	blood:
4	chr12:117442427..117445023-chr12:117448481..117451118,2	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10735100	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10735101	0.96[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10774895	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10774898	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10850730	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10850734	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10850742	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10850747	0.82[JPT][hapmap]
rs10850751	0.88[JPT][hapmap]
rs11068276	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11068292	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11834817	0.89[JPT][hapmap]
rs1472523	0.89[JPT][hapmap]
rs2062528	0.94[JPT][hapmap]
rs2173654	0.94[JPT][hapmap]
rs2291916	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2393113	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4766816	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4766823	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4767477	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4767486	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6490106	0.84[JPT][hapmap]
rs7133090	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7297303	0.88[JPT][hapmap]
rs7302127	0.87[CEU][hapmap]
rs7486428	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7487081	0.82[CEU][hapmap]
rs7958680	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7962875	0.95[EUR][1000 genomes]
rs7964668	0.88[JPT][hapmap]
rs9634171	0.94[JPT][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	nsv832524	chr12:117314110-117496576	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv519118	chr12:117386085-117521180	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv899541	chr12:117414974-117497066	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117384800-117450400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr12:117387800-117463600	Weak transcription	HMEC	breast
3	chr12:117393800-117471000	Weak transcription	Small Intestine	intestine
4	chr12:117408400-117452200	Weak transcription	Thymus	Thymus
5	chr12:117411600-117451800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr12:117417200-117452400	Weak transcription	Psoas Muscle	Psoas
7	chr12:117417400-117453600	Weak transcription	GM12878-XiMat	blood
8	chr12:117418400-117444600	Weak transcription	HUVEC	blood vessel
9	chr12:117426200-117466600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr12:117426800-117445600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr12:117427200-117442800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr12:117427800-117443400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr12:117428200-117447600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr12:117428600-117442800	Weak transcription	NHDF-Ad	bronchial
15	chr12:117432000-117446200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr12:117432200-117444200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr12:117432200-117446400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr12:117432600-117445800	Strong transcription	Fetal Muscle Leg	muscle
19	chr12:117432800-117444600	Strong transcription	Fetal Stomach	stomach
20	chr12:117434200-117443200	Weak transcription	Hela-S3	cervix
21	chr12:117434200-117449800	Weak transcription	NHEK	skin
22	chr12:117434400-117442800	Weak transcription	Primary hematopoietic stem cells	blood
23	chr12:117434800-117443000	Weak transcription	Brain Anterior Caudate	brain
24	chr12:117434800-117444200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr12:117435600-117449800	Weak transcription	Stomach Mucosa	stomach
26	chr12:117436800-117445600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr12:117437000-117447800	Weak transcription	Colon Smooth Muscle	Colon
28	chr12:117437400-117451600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr12:117437600-117445800	Strong transcription	Primary B cells from cord blood	blood
30	chr12:117437600-117447000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr12:117437600-117448000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr12:117437800-117442800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr12:117438000-117443200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr12:117438000-117445600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr12:117438200-117444800	Strong transcription	Duodenum Mucosa	Duodenum
36	chr12:117438200-117445600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr12:117438200-117445800	Strong transcription	Primary T cells from cord blood	blood
38	chr12:117438200-117447600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr12:117438600-117446200	Strong transcription	Primary B cells from peripheral blood	blood
40	chr12:117438800-117445200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr12:117439000-117445400	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr12:117439200-117447000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr12:117439200-117447200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr12:117439400-117443400	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr12:117439400-117444600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr12:117439400-117445600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:117440000-117444600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr12:117440200-117443200	Weak transcription	Brain Angular Gyrus	brain
49	chr12:117440400-117443200	Weak transcription	Right Ventricle	heart
50	chr12:117440400-117452200	Weak transcription	Brain Cingulate Gyrus	brain

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