Variant report

Variant	rs198646
Chromosome Location	chr6:143156612-143156613
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:143156192..143158401-chr6:143265953..143267807,2	MCF-7	breast:
2	chr6:143155142..143156982-chr6:143162746..143165321,2	MCF-7	breast:
3	chr6:143152862..143155335-chr6:143156490..143158153,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000010818	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1040439	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs109301	0.82[AMR][1000 genomes]
rs11155267	0.82[AMR][1000 genomes]
rs198653	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs198657	0.82[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs198668	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs198675	0.82[AMR][1000 genomes]
rs198682	0.81[AMR][1000 genomes]
rs2142939	0.82[CEU][hapmap];0.80[CHB][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2328386	0.82[CEU][hapmap];0.84[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2328387	0.82[CEU][hapmap];0.80[CHB][hapmap];0.85[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs493985	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs573352	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs592503	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7752766	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7763660	0.83[ASN][1000 genomes]
rs926372	0.82[CEU][hapmap];0.80[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9376711	0.82[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830829	chr6:143058408-143218077	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:143143400-143157400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr6:143143400-143159600	Weak transcription	HepG2	liver
3	chr6:143143400-143160600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr6:143144000-143165800	Weak transcription	Liver	Liver
5	chr6:143144600-143163000	Weak transcription	Dnd41	blood
6	chr6:143144600-143163200	Weak transcription	Fetal Thymus	thymus
7	chr6:143144800-143162400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr6:143144800-143163000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:143144800-143166800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr6:143149200-143166000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr6:143149400-143163200	Weak transcription	Adipose Nuclei	Adipose
12	chr6:143149400-143163600	Weak transcription	Fetal Lung	lung
13	chr6:143149600-143165600	Weak transcription	Colon Smooth Muscle	Colon
14	chr6:143151000-143158000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:143151400-143163200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr6:143152000-143163400	Weak transcription	Thymus	Thymus
17	chr6:143152200-143160600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr6:143152400-143158400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr6:143152400-143160600	Weak transcription	Left Ventricle	heart
20	chr6:143152400-143160600	Weak transcription	Spleen	Spleen
21	chr6:143152400-143160800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr6:143152400-143160800	Weak transcription	Right Ventricle	heart
23	chr6:143152600-143159200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr6:143152600-143160600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:143152600-143160600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr6:143152600-143163000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr6:143152800-143157800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr6:143152800-143160200	Weak transcription	Fetal Intestine Small	intestine
29	chr6:143152800-143163600	Weak transcription	Fetal Stomach	stomach
30	chr6:143154200-143157200	Strong transcription	Primary B cells from cord blood	blood
31	chr6:143154200-143160600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr6:143154400-143160600	Weak transcription	Psoas Muscle	Psoas
33	chr6:143154600-143156800	Weak transcription	Brain Anterior Caudate	brain
34	chr6:143154600-143156800	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr6:143154600-143158000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr6:143154600-143159200	Weak transcription	Hela-S3	cervix
37	chr6:143154600-143159400	Weak transcription	A549	lung
38	chr6:143154600-143160400	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr6:143154600-143160600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr6:143154600-143163000	Weak transcription	Primary hematopoietic stem cells	blood
41	chr6:143154600-143163600	Weak transcription	Aorta	Aorta
42	chr6:143154800-143158200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr6:143154800-143158200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr6:143154800-143159600	Weak transcription	Stomach Mucosa	stomach
45	chr6:143154800-143160600	Weak transcription	HSMM	muscle
46	chr6:143155000-143159200	Weak transcription	HMEC	breast
47	chr6:143155000-143160000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr6:143155000-143160000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr6:143155000-143162600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr6:143155200-143159000	Weak transcription	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links