Variant report

Variant	rs6573983
Chromosome Location	chr14:71290757-71290758
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	chr14:71288544..71291419-chr14:71373851..71375362,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PCNX-4	chr14:71290537-71290888	NONHSAT037594

Variant related genes	Relation type
ENSG00000100731	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10083428	0.81[EUR][1000 genomes]
rs10483834	0.82[CEU][hapmap]
rs11847356	0.83[EUR][1000 genomes]
rs11847373	0.85[EUR][1000 genomes]
rs17108554	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17176985	0.83[CEU][hapmap]
rs17177014	0.83[CEU][hapmap]
rs17766512	0.83[CEU][hapmap]
rs17766551	0.82[CEU][hapmap]
rs17766661	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs1859460	0.81[EUR][1000 genomes]
rs1859461	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs1859462	0.82[AMR][1000 genomes]
rs2023954	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs4595741	0.83[CEU][hapmap]
rs4899372	0.83[EUR][1000 genomes]
rs4899373	0.83[EUR][1000 genomes]
rs4899374	0.87[CEU][hapmap];0.81[GIH][hapmap]
rs4902857	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs4902858	0.81[EUR][1000 genomes]
rs4902859	0.81[EUR][1000 genomes]
rs61990519	0.80[EUR][1000 genomes]
rs61990520	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61990521	0.81[EUR][1000 genomes]
rs61990523	0.81[EUR][1000 genomes]
rs61990526	0.83[EUR][1000 genomes]
rs61990527	0.86[EUR][1000 genomes]
rs61990550	0.82[EUR][1000 genomes]
rs61990551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6573982	0.85[EUR][1000 genomes]
rs7141204	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7151024	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs7157405	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs72721952	0.83[EUR][1000 genomes]
rs757570	0.80[EUR][1000 genomes]
rs8018972	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8019053	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8020803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8022621	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039460	chr14:71176898-71371125	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv1041980	chr14:71196358-71767339	Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv542125	chr14:71196358-71767339	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1035416	chr14:71212882-71623271	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv542126	chr14:71212882-71623271	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv1049741	chr14:71233043-71462509	Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1037839	chr14:71263886-71625114	Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv542127	chr14:71263886-71625114	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv1038007	chr14:71269747-71667680	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71289800-71293600	Weak transcription	Liver	Liver
2	chr14:71289800-71294000	Weak transcription	HSMM	muscle
3	chr14:71290000-71290800	Enhancers	Fetal Intestine Small	intestine
4	chr14:71290000-71291200	Weak transcription	Ovary	ovary
5	chr14:71290000-71291400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr14:71290000-71294000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr14:71290000-71294000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr14:71290000-71294000	Weak transcription	Duodenum Mucosa	Duodenum
9	chr14:71290000-71298600	Weak transcription	Right Atrium	heart
10	chr14:71290200-71290800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
11	chr14:71290400-71291400	Weak transcription	Fetal Intestine Large	intestine
12	chr14:71290600-71290800	Bivalent/Poised TSS	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links