Variant report

Variant	rs12194742
Chromosome Location	chr6:13234231-13234232
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:13232923..13234560-chr6:13313162..13315905,2	K562	blood:
2	chr6:13233464..13235028-chr6:13327607..13330085,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145979	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1150617	0.93[ASN][1000 genomes]
rs1150619	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1223393	0.81[CEU][hapmap];0.85[GIH][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs1232381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1232382	0.86[ASW][hapmap]
rs182148	0.85[GIH][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs202025	0.91[EUR][1000 genomes]
rs202027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs202060	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs202064	0.81[CEU][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs202068	0.84[EUR][1000 genomes]
rs202069	0.80[GIH][hapmap];0.87[JPT][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs202070	0.83[JPT][hapmap]
rs202071	0.83[JPT][hapmap]
rs202072	0.83[JPT][hapmap]
rs202073	0.83[JPT][hapmap]
rs366904	0.87[JPT][hapmap]
rs453695	0.81[CEU][hapmap];0.83[CHB][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs536208	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432849	chr6:13225077-13253733	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13208200-13239800	Weak transcription	Brain Substantia Nigra	brain
2	chr6:13217800-13242400	Weak transcription	Pancreas	Pancrea
3	chr6:13218200-13235000	Weak transcription	Adipose Nuclei	Adipose
4	chr6:13218400-13241000	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr6:13218600-13234400	Weak transcription	HSMM	muscle
6	chr6:13227800-13235600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr6:13227800-13238600	Strong transcription	Stomach Smooth Muscle	stomach
8	chr6:13227800-13240000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr6:13227800-13244000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr6:13228000-13236000	Weak transcription	Fetal Brain Male	brain
11	chr6:13228400-13237200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr6:13229200-13240000	Weak transcription	Fetal Lung	lung
13	chr6:13229400-13248200	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr6:13230000-13236000	Strong transcription	Brain Anterior Caudate	brain
15	chr6:13230000-13239800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr6:13230200-13235000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr6:13230200-13242400	Weak transcription	Fetal Intestine Small	intestine
18	chr6:13230600-13253400	Weak transcription	Spleen	Spleen
19	chr6:13230800-13248000	Weak transcription	Fetal Muscle Leg	muscle
20	chr6:13231200-13248200	Weak transcription	Fetal Stomach	stomach
21	chr6:13232200-13235600	Strong transcription	Lung	lung
22	chr6:13232800-13239800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr6:13232800-13240000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr6:13232800-13240200	Weak transcription	Brain Hippocampus Middle	brain
25	chr6:13232800-13243800	Weak transcription	Fetal Brain Female	brain
26	chr6:13233200-13234400	Genic enhancers	Left Ventricle	heart
27	chr6:13233200-13234600	Enhancers	Placenta	Placenta
28	chr6:13233200-13236200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr6:13233200-13239800	Weak transcription	Brain Angular Gyrus	brain
30	chr6:13233200-13256000	Weak transcription	Right Ventricle	heart
31	chr6:13233400-13236000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr6:13233600-13236600	Weak transcription	Primary hematopoietic stem cells	blood
33	chr6:13234000-13234600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr6:13234000-13234600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr6:13234000-13234800	Genic enhancers	Fetal Heart	heart
36	chr6:13234000-13234800	Enhancers	GM12878-XiMat	blood
37	chr6:13234000-13235200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr6:13234000-13235200	Enhancers	HSMMtube	muscle
39	chr6:13234000-13236000	Strong transcription	Brain Germinal Matrix	brain
40	chr6:13234000-13236200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr6:13234200-13234600	Enhancers	Aorta	Aorta
42	chr6:13234200-13234800	Enhancers	HMEC	breast
43	chr6:13234200-13235200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr6:13234200-13235400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr6:13234200-13235600	Enhancers	Liver	Liver
46	chr6:13234200-13235600	Enhancers	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links