Variant report

Variant	rs12194771
Chromosome Location	chr6:11539337-11539338
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	chr19:47291454..47293291-chr6:11538059..11540323,2	MCF-7	breast:
2	chr6:11539069..11540912-chr6:11545787..11548453,2	K562	blood:

Variant related genes	Relation type
ENSG00000105281	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10807114	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10807115	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10947398	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11751884	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11752836	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11755780	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11756371	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12192094	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12198765	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12198774	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12198950	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12200391	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12200454	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12528839	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs145176	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2025184	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2025185	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs211510	0.88[ASN][1000 genomes]
rs2758307	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2807964	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs295051	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs295059	0.88[ASN][1000 genomes]
rs295060	0.88[ASN][1000 genomes]
rs295061	0.88[ASN][1000 genomes]
rs295062	0.87[ASN][1000 genomes]
rs295063	0.87[ASN][1000 genomes]
rs295064	0.87[ASN][1000 genomes]
rs3857556	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4711306	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4713593	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4713594	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4713618	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs493183	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs505685	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs586117	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs588062	0.88[ASN][1000 genomes]
rs594164	0.87[ASN][1000 genomes]
rs595877	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61570488	0.81[ASN][1000 genomes]
rs616729	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs651001	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6901328	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6907796	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6908807	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6913697	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6914208	0.84[EUR][1000 genomes]
rs6914420	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6915153	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6915366	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6916089	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6930371	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6932324	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6940859	0.80[EUR][1000 genomes]
rs6941011	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6941700	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7749662	0.83[ASN][1000 genomes]
rs7770004	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9348892	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9348895	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9348896	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9357154	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9366805	0.81[ASN][1000 genomes]
rs9366806	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9380310	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9380311	0.81[ASN][1000 genomes]
rs9380315	0.81[ASN][1000 genomes]
rs9394102	0.81[ASN][1000 genomes]
rs9394117	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9394146	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9394154	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021078	chr6:10819083-11558560	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv538135	chr6:10819083-11558560	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv432848	chr6:11371614-11560114	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv600989	chr6:11509323-11581990	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	esv3323084	chr6:11535666-11540364	Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11536400-11540400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr6:11536800-11539400	Active TSS	H9 Cell Line	embryonic stem cell
3	chr6:11536800-11539400	Active TSS	Fetal Intestine Small	intestine
4	chr6:11536800-11539600	Active TSS	A549	lung
5	chr6:11536800-11540000	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr6:11536800-11540400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr6:11537000-11539400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:11537000-11539600	Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr6:11537000-11540000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr6:11537000-11540000	Active TSS	Brain Anterior Caudate	brain
11	chr6:11537000-11540000	Active TSS	Right Atrium	heart
12	chr6:11537000-11540200	Active TSS	Brain Cingulate Gyrus	brain
13	chr6:11537000-11540400	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr6:11537000-11540600	Active TSS	Brain Angular Gyrus	brain
15	chr6:11537200-11539400	Active TSS	HSMMtube	muscle
16	chr6:11537400-11539400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr6:11537400-11539400	Active TSS	Primary T cells from cord blood	blood
18	chr6:11537400-11539400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr6:11537400-11539400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr6:11537400-11539400	Active TSS	Fetal Muscle Leg	muscle
21	chr6:11537400-11539400	Active TSS	Fetal Thymus	thymus
22	chr6:11537400-11539400	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr6:11537400-11539400	Active TSS	Rectal Smooth Muscle	rectum
24	chr6:11537400-11539800	Active TSS	Cortex derived primary cultured neurospheres	brain
25	chr6:11537400-11540000	Active TSS	Monocytes-CD14+_RO01746	blood
26	chr6:11537400-11540200	Active TSS	Primary monocytes fromperipheralblood	blood
27	chr6:11537400-11543200	Active TSS	GM12878-XiMat	blood
28	chr6:11537600-11539400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr6:11538000-11539400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
30	chr6:11538200-11539400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
31	chr6:11538400-11539400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
32	chr6:11538600-11539400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
33	chr6:11538600-11539400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
34	chr6:11538600-11539400	Flanking Active TSS	Primary B cells from cord blood	blood
35	chr6:11538600-11539400	Flanking Active TSS	Adipose Nuclei	Adipose
36	chr6:11538800-11539400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr6:11538800-11539400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr6:11538800-11539400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr6:11538800-11539400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
40	chr6:11538800-11539400	Flanking Active TSS	HUVEC	blood vessel
41	chr6:11538800-11539600	Enhancers	Fetal Heart	heart
42	chr6:11538800-11539800	Active TSS	Fetal Brain Male	brain
43	chr6:11539000-11539400	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
44	chr6:11539000-11539400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
45	chr6:11539000-11539400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
46	chr6:11539000-11539400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
47	chr6:11539000-11539400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
48	chr6:11539000-11539400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr6:11539000-11539400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr6:11539000-11539400	Flanking Active TSS	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links