Variant report

Variant	rs57535407
Chromosome Location	chr11:46570286-46570287
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:46570272-46570346	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:46568146..46571770-chr11:46637257..46640089,4	MCF-7	breast:

Variant related genes	Relation type
AMBRA1	TF binding region
ENSG00000175224	Chromatin interaction
ENSG00000180423	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10160701	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10838602	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11038897	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11038900	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11038906	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11038914	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11038919	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11038927	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11819869	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12272795	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12283172	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12292425	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12295266	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12573978	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12574250	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12574668	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12575519	0.96[EUR][1000 genomes]
rs12576115	0.95[EUR][1000 genomes]
rs12576317	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12576359	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12577142	0.95[EUR][1000 genomes]
rs12578042	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1472001	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1489192	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16938506	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17197116	0.97[ASN][1000 genomes]
rs2046768	0.98[EUR][1000 genomes]
rs2067482	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2171667	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2171668	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2279465	0.98[EUR][1000 genomes]
rs2291487	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2864072	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2864076	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2902858	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34406563	0.95[EUR][1000 genomes]
rs35324223	0.84[EUR][1000 genomes]
rs35623865	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3740974	0.98[EUR][1000 genomes]
rs3740977	0.99[EUR][1000 genomes]
rs3802888	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4307676	0.87[EUR][1000 genomes]
rs55657382	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55661562	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55750336	0.97[ASN][1000 genomes]
rs55896955	0.80[EUR][1000 genomes]
rs58147945	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59319338	0.97[EUR][1000 genomes]
rs60722866	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60932698	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61882674	0.84[EUR][1000 genomes]
rs61882678	0.90[EUR][1000 genomes]
rs61882682	0.98[EUR][1000 genomes]
rs61882683	0.93[EUR][1000 genomes]
rs61882691	0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61882701	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61882702	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61882706	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61882709	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61882710	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61882711	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61882712	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61882720	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882743	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882746	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882748	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882750	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882756	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61882757	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61882758	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61884262	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61884264	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61884271	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61884273	0.87[EUR][1000 genomes]
rs61884274	0.87[EUR][1000 genomes]
rs61884292	0.80[EUR][1000 genomes]
rs6485682	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6485685	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7108770	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7109698	0.81[EUR][1000 genomes]
rs7112229	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7122039	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7125907	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7126316	0.86[EUR][1000 genomes]
rs7126343	0.87[EUR][1000 genomes]
rs7127529	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7128092	0.86[EUR][1000 genomes]
rs7130141	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73449983	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7481312	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7484002	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs756343	0.97[ASN][1000 genomes]
rs7924401	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7930103	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7932866	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7936413	0.98[EUR][1000 genomes]
rs7946705	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7951579	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7951870	0.97[EUR][1000 genomes]
rs876701	0.91[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	nsv1044225	chr11:46472580-46771102	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv541030	chr11:46472580-46771102	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1046990	chr11:46501436-46669636	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv541031	chr11:46501436-46669636	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv897321	chr11:46515902-46673344	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:46559400-46575200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr11:46559400-46575400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:46561200-46570600	Strong transcription	Primary B cells from cord blood	blood
4	chr11:46561600-46570400	Strong transcription	Fetal Thymus	thymus
5	chr11:46564000-46575000	Weak transcription	Right Atrium	heart
6	chr11:46564600-46574800	Weak transcription	Stomach Mucosa	stomach
7	chr11:46565000-46575200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr11:46565000-46579200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr11:46566000-46579200	Weak transcription	Fetal Heart	heart
10	chr11:46566600-46570800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr11:46566600-46575200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr11:46567400-46571800	Weak transcription	K562	blood
13	chr11:46567400-46574800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr11:46567400-46574800	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr11:46567400-46575000	Weak transcription	HSMMtube	muscle
16	chr11:46567400-46576200	Weak transcription	Aorta	Aorta
17	chr11:46567400-46579000	Weak transcription	Pancreas	Pancrea
18	chr11:46567400-46579200	Weak transcription	Gastric	stomach
19	chr11:46567800-46576200	Weak transcription	Colonic Mucosa	Colon
20	chr11:46568000-46575000	Weak transcription	Small Intestine	intestine
21	chr11:46568000-46576400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr11:46568200-46574800	Weak transcription	NHLF	lung
23	chr11:46568200-46575400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr11:46568200-46575400	Weak transcription	Fetal Kidney	kidney
25	chr11:46568400-46575000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr11:46568400-46575000	Weak transcription	NHEK	skin
27	chr11:46568600-46575000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr11:46568800-46575000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr11:46568800-46575000	Weak transcription	Left Ventricle	heart
30	chr11:46568800-46575000	Weak transcription	Right Ventricle	heart
31	chr11:46568800-46575200	Weak transcription	Brain Angular Gyrus	brain
32	chr11:46568800-46575400	Weak transcription	Brain Cingulate Gyrus	brain
33	chr11:46568800-46576400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr11:46568800-46579000	Weak transcription	Lung	lung
35	chr11:46568800-46582200	Weak transcription	Fetal Stomach	stomach
36	chr11:46568800-46611000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr11:46568800-46612600	Weak transcription	Brain Germinal Matrix	brain
38	chr11:46569000-46574600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr11:46569000-46574800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr11:46569000-46574800	Weak transcription	NH-A	brain
41	chr11:46569000-46575000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr11:46569000-46575000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr11:46569000-46575000	Weak transcription	Osteobl	bone
44	chr11:46569000-46575200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr11:46569000-46575200	Weak transcription	Brain Substantia Nigra	brain
46	chr11:46569000-46576400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr11:46569000-46579000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr11:46569000-46579200	Weak transcription	Esophagus	oesophagus
49	chr11:46569000-46579200	Weak transcription	Spleen	Spleen
50	chr11:46569200-46571200	Weak transcription	Fetal Brain Female	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links