Variant report

Variant	rs12866391
Chromosome Location	chr13:30796838-30796839
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:30796105..30798319-chr13:30802158..30804551,2	MCF-7	breast:
2	chr13:30796832..30799585-chr13:30801538..30805408,3	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12585819	0.86[ASN][1000 genomes]
rs12870695	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs17632858	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs2031998	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2149970	0.97[ASN][1000 genomes]
rs2149971	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2149973	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs28805029	0.88[ASN][1000 genomes]
rs35331241	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35963596	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3803272	1.00[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs3825532	0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs3825533	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61946958	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7328946	0.85[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7331974	0.82[YRI][hapmap]
rs7987688	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9550538	1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs9550539	1.00[CHB][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];0.80[TSI][hapmap];0.88[ASN][1000 genomes]
rs9550540	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9550541	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9551867	0.90[CHB][hapmap]
rs9551868	0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9551875	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9551879	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9551882	0.87[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832572	chr13:30650005-30835256	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30754000-30798800	Weak transcription	Brain Anterior Caudate	brain
2	chr13:30765600-30807000	Weak transcription	Gastric	stomach
3	chr13:30766400-30804400	Weak transcription	Duodenum Mucosa	Duodenum
4	chr13:30768600-30798800	Weak transcription	HMEC	breast
5	chr13:30770000-30799200	Weak transcription	HSMMtube	muscle
6	chr13:30770600-30803200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr13:30774400-30812600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr13:30774600-30802800	Weak transcription	Lung	lung
9	chr13:30774600-30805200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr13:30775000-30803000	Weak transcription	Esophagus	oesophagus
11	chr13:30777200-30799000	Weak transcription	Brain Angular Gyrus	brain
12	chr13:30780200-30801000	Weak transcription	Pancreas	Pancrea
13	chr13:30782600-30798400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr13:30783200-30799000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr13:30783400-30798000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr13:30783800-30797800	Weak transcription	Primary T cells from cord blood	blood
17	chr13:30790000-30807000	Weak transcription	Small Intestine	intestine
18	chr13:30790800-30799000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr13:30791000-30797800	Weak transcription	Colonic Mucosa	Colon
20	chr13:30791000-30798400	Weak transcription	Right Ventricle	heart
21	chr13:30791000-30799000	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr13:30791000-30799000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr13:30791000-30799000	Weak transcription	Aorta	Aorta
24	chr13:30791000-30799000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr13:30791000-30802600	Weak transcription	Brain Cingulate Gyrus	brain
26	chr13:30791000-30802600	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr13:30791000-30807200	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr13:30791000-30808800	Weak transcription	Brain Hippocampus Middle	brain
29	chr13:30791000-30811600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr13:30791000-30831400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr13:30791200-30798800	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr13:30792400-30802600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr13:30794000-30801200	Weak transcription	Colon Smooth Muscle	Colon
34	chr13:30794400-30797200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr13:30795000-30800000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr13:30795200-30798000	Strong transcription	NHDF-Ad	bronchial
37	chr13:30795400-30797000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr13:30795400-30799000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr13:30795600-30797000	Strong transcription	Osteobl	bone
40	chr13:30795600-30797400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr13:30795600-30798000	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr13:30795800-30797000	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
43	chr13:30795800-30797000	Strong transcription	Stomach Smooth Muscle	stomach
44	chr13:30795800-30797400	Strong transcription	Fetal Muscle Trunk	muscle
45	chr13:30795800-30797400	Strong transcription	Left Ventricle	heart
46	chr13:30795800-30798800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr13:30795800-30798800	ZNF genes & repeats	Fetal Thymus	thymus
48	chr13:30795800-30805600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr13:30796000-30797000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
50	chr13:30796000-30797400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood

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