Variant report

Variant	rs12664994
Chromosome Location	chr6:38257774-38257775
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	chr6:38256129..38257885-chr6:38259661..38261531,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10484930	0.81[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10484931	0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12055513	0.81[JPT][hapmap]
rs12173290	0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12524225	0.82[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12527432	0.91[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12529549	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12660323	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs16890552	0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs16890561	0.81[JPT][hapmap]
rs2395697	0.82[JPT][hapmap]
rs4711531	0.91[CHB][hapmap];0.91[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4711532	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4714139	0.87[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4714141	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4714145	0.91[JPT][hapmap]
rs57012325	0.90[ASN][1000 genomes]
rs57934228	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs59624393	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60500173	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6938840	0.81[JPT][hapmap]
rs714930	0.83[JPT][hapmap]
rs73422824	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs73422833	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs73730927	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73730928	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7771835	0.82[JPT][hapmap]
rs871182	0.87[AMR][1000 genomes]
rs871184	0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9296243	0.91[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs9349065	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9349071	0.82[JPT][hapmap]
rs9366951	0.97[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9366952	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9366956	0.81[JPT][hapmap]
rs9369044	0.95[CHB][hapmap];0.83[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9369045	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9369046	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9369047	0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9369052	0.82[JPT][hapmap]
rs9380728	0.91[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9380729	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9380730	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9380731	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9380732	0.94[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9380733	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9380736	0.82[JPT][hapmap]
rs9394483	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9394485	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9394487	0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9394490	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9394491	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv885818	chr6:38147745-38436317	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv885820	chr6:38166511-38468887	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38224400-38267600	Weak transcription	Primary T cells from cord blood	blood
2	chr6:38226400-38258000	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr6:38230800-38257800	Weak transcription	Pancreas	Pancrea
4	chr6:38238400-38258200	Weak transcription	Left Ventricle	heart
5	chr6:38238600-38258000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr6:38239400-38257800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr6:38239400-38259200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr6:38240000-38257800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr6:38241600-38258200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr6:38247200-38257800	Weak transcription	Fetal Kidney	kidney
11	chr6:38248400-38258400	Weak transcription	Colon Smooth Muscle	Colon
12	chr6:38249000-38258200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr6:38249200-38257800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr6:38249200-38258000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr6:38249200-38258000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr6:38249200-38258400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr6:38249200-38275600	Weak transcription	Fetal Brain Male	brain
18	chr6:38250600-38258200	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr6:38252400-38257800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr6:38256000-38258400	Weak transcription	Primary B cells from peripheral blood	blood
21	chr6:38256000-38263000	Weak transcription	Lung	lung
22	chr6:38256200-38257800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr6:38256200-38257800	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr6:38256200-38258000	Weak transcription	Primary B cells from cord blood	blood
25	chr6:38256200-38258000	Weak transcription	Brain Angular Gyrus	brain
26	chr6:38256200-38258200	Weak transcription	Brain Substantia Nigra	brain
27	chr6:38256200-38258400	Weak transcription	Ovary	ovary
28	chr6:38256200-38258400	Weak transcription	Stomach Smooth Muscle	stomach
29	chr6:38256400-38258000	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr6:38256400-38258000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr6:38256400-38259000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr6:38257400-38258600	Enhancers	Fetal Heart	heart
33	chr6:38257600-38258600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:38257600-38258600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr6:38257600-38258600	Enhancers	Brain Anterior Caudate	brain
36	chr6:38257600-38259000	Enhancers	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links