Variant report

Variant	rs1523743
Chromosome Location	chr4:119266964-119266965
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	chr4:119200552..119202977-chr4:119264974..119267166,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11947394	0.84[TSI][hapmap]
rs13122419	0.94[CEU][hapmap];0.81[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13145025	0.81[CEU][hapmap]
rs1573955	0.81[CEU][hapmap]
rs2138009	0.81[MEX][hapmap];0.82[TSI][hapmap]
rs34082171	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3828500	0.83[CEU][hapmap];0.87[TSI][hapmap]
rs4833572	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4834678	0.94[CEU][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56710957	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6825871	0.82[CEU][hapmap]
rs7690554	0.94[CEU][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs972813	0.83[CEU][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519017	chr4:118828807-119771481	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1009076	chr4:118949490-119269424	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1001236	chr4:118949490-119271243	Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	esv34038	chr4:119035124-119455391	Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv1001138	chr4:119095147-119461837	Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv537230	chr4:119095147-119461837	Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv1002771	chr4:119125361-119571237	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	nsv1003731	chr4:119138262-119506032	Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv482277	chr4:119261543-119408886	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv461631	chr4:119261939-119308603	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv595331	chr4:119261939-119308603	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1523743	SNHG8	cis	Skin Sun Exposed Lower leg	GTEx
rs1523743	UGT8	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119202800-119267200	Weak transcription	Stomach Mucosa	stomach
2	chr4:119229000-119267200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:119259400-119267000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr4:119259600-119267800	Weak transcription	Fetal Brain Male	brain
5	chr4:119261600-119272200	Weak transcription	Fetal Brain Female	brain
6	chr4:119261800-119267000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr4:119262000-119267000	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr4:119262000-119267000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr4:119262000-119267000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr4:119262200-119267000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr4:119262200-119267200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr4:119262400-119267000	Weak transcription	NHLF	lung
13	chr4:119262400-119268800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr4:119264400-119267800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr4:119265400-119267400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:119265600-119271600	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr4:119265800-119270800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr4:119266000-119267200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr4:119266000-119267400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr4:119266000-119267400	Enhancers	Muscle Satellite Cultured Cells	--
21	chr4:119266000-119267400	Enhancers	Osteobl	bone
22	chr4:119266000-119268200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr4:119266000-119270600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr4:119266000-119270800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr4:119266000-119270800	Enhancers	NHEK	skin
26	chr4:119266200-119267400	Enhancers	Fetal Intestine Small	intestine
27	chr4:119266200-119268000	Enhancers	HMEC	breast
28	chr4:119266400-119267200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:119266400-119267400	Enhancers	Fetal Intestine Large	intestine
30	chr4:119266400-119269000	Enhancers	NHDF-Ad	bronchial
31	chr4:119266800-119267200	Enhancers	Rectal Mucosa Donor 29	rectum
32	chr4:119266800-119268000	Enhancers	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links