Variant report

Variant	rs9475713
Chromosome Location	chr6:56386076-56386077
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:56385896..56387722-chr6:56406237..56408892,2	MCF-7	breast:
2	chr6:56379723..56396922-chr6:56400495..56411638,31	K562	blood:

Variant related genes	Relation type
ENSG00000151914	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs11753813	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes]
rs11756977	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11758339	0.93[GIH][hapmap];0.83[MEX][hapmap]
rs11759493	0.87[CEU][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs12527139	0.87[EUR][1000 genomes]
rs13194746	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13219448	0.83[AMR][1000 genomes]
rs1535610	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1535612	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16887974	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17825773	0.84[MEX][hapmap]
rs2064591	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2273972	0.93[GIH][hapmap];0.84[MEX][hapmap]
rs2273973	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs2273974	0.87[CEU][hapmap];0.81[JPT][hapmap]
rs2397226	0.82[JPT][hapmap]
rs4130060	0.87[CEU][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes]
rs4143827	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4143828	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs4236139	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4236140	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4236141	1.00[CEU][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4236142	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4236143	0.86[EUR][1000 genomes]
rs4236144	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs4236145	0.87[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4283892	0.87[CEU][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs4329120	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4346846	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4454141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4466244	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4472350	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4473850	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4499917	0.87[CEU][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4712132	0.87[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4712133	0.91[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4715625	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs4715626	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715627	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4715630	0.87[CEU][hapmap];0.89[GIH][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs4715631	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs594008	0.83[GIH][hapmap]
rs6459161	0.91[CEU][hapmap];0.93[GIH][hapmap];0.88[MEX][hapmap]
rs6904202	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6906792	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6907917	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6911502	0.89[GIH][hapmap];0.83[MEX][hapmap]
rs6914184	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6919608	0.94[ASW][hapmap];0.86[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.86[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6922770	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6939305	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71549713	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs721475	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7741295	0.87[CEU][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs7743011	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7749370	0.84[ASN][1000 genomes]
rs7755361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7755573	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7758054	0.87[EUR][1000 genomes]
rs7759875	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7760640	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7760695	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7761281	0.89[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes]
rs7762629	0.82[JPT][hapmap];0.84[EUR][1000 genomes]
rs9296848	0.87[CEU][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs9296849	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9296850	0.86[CEU][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9349826	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9357921	1.00[CEU][hapmap];0.82[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9357922	0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9370533	0.95[CEU][hapmap]
rs9370534	0.82[JPT][hapmap]
rs9370535	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs9382635	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9396213	0.86[CEU][hapmap];0.98[GIH][hapmap];0.83[MEX][hapmap]
rs9396214	0.82[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap]
rs9396218	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9396220	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9464389	0.89[EUR][1000 genomes]
rs9475709	0.89[EUR][1000 genomes]
rs9475711	0.85[ASN][1000 genomes]
rs9475714	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9475716	0.82[EUR][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	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830666	chr6:56243743-56419599	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv885912	chr6:56327849-56458836	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1016868	chr6:56376165-56417631	Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
5	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56341800-56407400	Weak transcription	Spleen	Spleen
2	chr6:56351800-56386800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:56362400-56391200	Weak transcription	Esophagus	oesophagus
4	chr6:56362800-56400200	Weak transcription	Colonic Mucosa	Colon
5	chr6:56363000-56402200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:56373000-56390800	Weak transcription	Placenta	Placenta
7	chr6:56374200-56387000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr6:56374200-56390800	Weak transcription	Lung	lung
9	chr6:56374200-56391000	Weak transcription	Right Atrium	heart
10	chr6:56374400-56386400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr6:56374400-56392000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr6:56374400-56396800	Weak transcription	Fetal Brain Female	brain
13	chr6:56374600-56390800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:56374600-56391200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:56374600-56395200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr6:56374600-56399600	Weak transcription	Fetal Thymus	thymus
17	chr6:56375000-56387000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr6:56376400-56407200	Weak transcription	Gastric	stomach
19	chr6:56376600-56389800	Weak transcription	A549	lung
20	chr6:56377200-56404200	Weak transcription	K562	blood
21	chr6:56377800-56388000	Strong transcription	GM12878-XiMat	blood
22	chr6:56378800-56386400	Weak transcription	NHEK	skin
23	chr6:56380400-56386600	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr6:56380400-56390400	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr6:56380600-56386600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr6:56380600-56390400	Weak transcription	Stomach Mucosa	stomach
27	chr6:56380600-56401200	Weak transcription	Psoas Muscle	Psoas
28	chr6:56380800-56386600	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr6:56381200-56386800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr6:56382000-56390400	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr6:56382400-56386400	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr6:56382400-56386400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr6:56382400-56386400	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr6:56382400-56387400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr6:56382600-56390800	Weak transcription	Aorta	Aorta
36	chr6:56382600-56391000	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr6:56382800-56386400	Weak transcription	NHDF-Ad	bronchial
38	chr6:56382800-56386600	Weak transcription	Brain Hippocampus Middle	brain
39	chr6:56382800-56388600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr6:56382800-56390800	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr6:56383200-56396400	Weak transcription	Brain Germinal Matrix	brain
42	chr6:56383200-56402400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr6:56383600-56388200	Weak transcription	NH-A	brain
44	chr6:56384000-56390800	Weak transcription	Right Ventricle	heart
45	chr6:56384400-56389000	Weak transcription	Osteobl	bone
46	chr6:56384400-56402200	Weak transcription	Small Intestine	intestine
47	chr6:56384600-56386200	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr6:56384600-56386200	Weak transcription	Fetal Stomach	stomach
49	chr6:56384600-56386200	Enhancers	HSMMtube	muscle
50	chr6:56384600-56386600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links