Variant report

Variant	rs476904
Chromosome Location	chr6:13383430-13383431
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13382356..13383974-chr6:13614219..13616340,2	MCF-7	breast:
2	chr6:13379880..13381834-chr6:13381972..13383883,2	MCF-7	breast:
3	chr6:13383245..13384081-chr6:13397182..13397976,2	MCF-7	breast:
4	chr6:13355357..13357068-chr6:13380690..13383506,2	MCF-7	breast:
5	chr6:13381851..13383974-chr6:13486160..13487948,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000237786	Chromatin interaction
ENSG00000225921	Chromatin interaction
ENSG00000261071	Chromatin interaction
ENSG00000187461	Chromatin interaction
ENSG00000145990	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10807431	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs10807432	0.86[EUR][1000 genomes]
rs10948650	0.97[EUR][1000 genomes]
rs12153966	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs2439536	1.00[CEU][hapmap];0.84[CHB][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2496139	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2496160	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2496161	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2496162	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2496173	1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28813108	0.87[EUR][1000 genomes]
rs4711978	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs474159	0.88[EUR][1000 genomes]
rs489396	1.00[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs491278	1.00[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs492433	0.90[EUR][1000 genomes]
rs501987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs510932	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs516003	0.92[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.86[TSI][hapmap];0.92[EUR][1000 genomes]
rs517803	0.83[ASW][hapmap];0.92[CEU][hapmap];0.84[CHB][hapmap];0.80[CHD][hapmap];0.86[GIH][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs524118	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs531256	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs548119	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs552655	0.90[EUR][1000 genomes]
rs553671	0.93[EUR][1000 genomes]
rs553948	0.88[EUR][1000 genomes]
rs560396	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs564174	0.91[EUR][1000 genomes]
rs570315	0.92[CEU][hapmap];0.84[GIH][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs573109	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs575709	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs579028	0.91[EUR][1000 genomes]
rs7742713	0.80[YRI][hapmap]
rs7760579	0.92[CEU][hapmap];0.84[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];0.82[TSI][hapmap];0.91[EUR][1000 genomes]
rs7770078	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs821276	0.89[EUR][1000 genomes]
rs821277	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs9357708	1.00[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9367440	0.91[CEU][hapmap];0.83[CHB][hapmap];0.89[EUR][1000 genomes]
rs9474036	0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1034016	chr6:13248122-13418225	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats 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	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13365800-13385400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:13366000-13386800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:13368000-13404600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr6:13368400-13386600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:13376800-13386600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:13376800-13395200	Weak transcription	NHEK	skin
7	chr6:13377800-13395600	Weak transcription	Aorta	Aorta
8	chr6:13378600-13383600	Enhancers	GM12878-XiMat	blood
9	chr6:13379200-13386600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr6:13379400-13383600	Weak transcription	Spleen	Spleen
11	chr6:13380200-13383600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:13380200-13389400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:13381000-13385800	Enhancers	Primary B cells from peripheral blood	blood
14	chr6:13381200-13383600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr6:13381200-13383600	Weak transcription	Fetal Kidney	kidney
16	chr6:13381200-13384000	Weak transcription	Right Ventricle	heart
17	chr6:13381400-13383600	Weak transcription	Brain Angular Gyrus	brain
18	chr6:13381400-13383600	Weak transcription	HepG2	liver
19	chr6:13381800-13383600	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr6:13381800-13383800	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr6:13381800-13384600	Enhancers	Primary B cells from cord blood	blood
22	chr6:13381800-13395400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr6:13382000-13383800	Weak transcription	Colonic Mucosa	Colon
24	chr6:13382000-13383800	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr6:13382000-13385200	Weak transcription	K562	blood
26	chr6:13382000-13386600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr6:13382200-13383600	Weak transcription	Small Intestine	intestine
28	chr6:13382200-13384200	Weak transcription	Left Ventricle	heart
29	chr6:13382200-13384800	Weak transcription	Right Atrium	heart
30	chr6:13382400-13383600	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr6:13382400-13383600	Weak transcription	HMEC	breast
32	chr6:13382400-13386600	Weak transcription	Lung	lung
33	chr6:13382400-13397600	Weak transcription	Esophagus	oesophagus
34	chr6:13382800-13384600	Enhancers	Monocytes-CD14+_RO01746	blood
35	chr6:13382800-13385600	Enhancers	Liver	Liver
36	chr6:13383200-13383600	Enhancers	Duodenum Mucosa	Duodenum
37	chr6:13383200-13384200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr6:13383200-13384200	Enhancers	Primary neutrophils fromperipheralblood	blood
39	chr6:13383200-13384600	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr6:13383400-13383800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr6:13383400-13383800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr6:13383400-13383800	Enhancers	Brain Anterior Caudate	brain
43	chr6:13383400-13383800	Enhancers	Pancreatic Islets	Pancreatic Islet
44	chr6:13383400-13384000	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr6:13383400-13384000	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr6:13383400-13384000	Enhancers	Brain Substantia Nigra	brain
47	chr6:13383400-13384000	Enhancers	Fetal Lung	lung
48	chr6:13383400-13384000	Enhancers	Psoas Muscle	Psoas
49	chr6:13383400-13384000	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr6:13383400-13384200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links