Variant report

Variant	rs263119
Chromosome Location	chr6:142892729-142892730
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	chr6:142885913..142888379-chr6:142890685..142893143,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1098071	0.88[EUR][1000 genomes]
rs166401	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs171913	0.87[EUR][1000 genomes]
rs183799	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs187810	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs190522	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs190523	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs196353	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2077836	0.86[EUR][1000 genomes]
rs263103	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs263104	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs263105	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs263107	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs263113	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs263114	0.88[EUR][1000 genomes]
rs263115	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs263116	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs263120	0.90[EUR][1000 genomes]
rs263121	0.90[EUR][1000 genomes]
rs263122	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs263124	0.82[EUR][1000 genomes]
rs263126	0.82[EUR][1000 genomes]
rs263130	0.86[EUR][1000 genomes]
rs263131	0.80[EUR][1000 genomes]
rs263154	0.89[EUR][1000 genomes]
rs263155	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs263156	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs263165	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs263166	0.87[EUR][1000 genomes]
rs263167	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs263168	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs263171	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs263172	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs263174	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs263176	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs605790	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs839554	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs839556	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]

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	nsv949088	chr6:142561402-143128849	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1023426	chr6:142813845-142940262	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv830827	chr6:142840734-143015005	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv520479	chr6:142869099-142908146	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142888000-142892800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr6:142888400-142893400	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr6:142889200-142893600	Enhancers	Dnd41	blood
4	chr6:142889400-142893200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:142889800-142893400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:142891200-142893400	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr6:142891400-142893800	Enhancers	Primary T cells from cord blood	blood
8	chr6:142891600-142892800	Enhancers	NHEK	skin
9	chr6:142891600-142895200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:142892000-142893000	Weak transcription	Stomach Mucosa	stomach
11	chr6:142892000-142893200	Weak transcription	Fetal Intestine Small	intestine
12	chr6:142892200-142893400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr6:142892200-142895200	Weak transcription	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links