Variant report

Variant	rs7157671
Chromosome Location	chr14:25423947-25423948
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:25422906..25425550-chr14:25438493..25441061,2	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12893349	0.86[CEU][hapmap];0.89[CHB][hapmap];0.88[GIH][hapmap];0.82[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2057500	0.89[CHB][hapmap]
rs2146915	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2332460	0.86[CEU][hapmap];0.95[CHB][hapmap];0.88[GIH][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28466581	0.85[AMR][1000 genomes]
rs4981565	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4983036	0.84[CHB][hapmap]
rs4983039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9671254	0.95[CHB][hapmap];0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041336	chr14:24726564-25527319	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542000	chr14:24726564-25527319	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv901504	chr14:25184210-25646203	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv901508	chr14:25365505-25451903	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv1041051	chr14:25388230-25480511	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1047792	chr14:25388933-25503799	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv901509	chr14:25398571-25743484	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7157671	RNASE3	cis	parietal	SCAN
rs7157671	CPNE6	cis	cerebellum	SCAN
rs7157671	RIPK3	cis	parietal	SCAN
rs7157671	GMPR2	cis	cerebellum	SCAN
rs7157671	RNF31	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:25412600-25426600	Weak transcription	Fetal Intestine Small	intestine
2	chr14:25412600-25426800	Weak transcription	Fetal Intestine Large	intestine
3	chr14:25414200-25424400	Weak transcription	Pancreas	Pancrea
4	chr14:25421800-25424000	Enhancers	Brain Hippocampus Middle	brain
5	chr14:25422000-25424600	Enhancers	Brain Inferior Temporal Lobe	brain
6	chr14:25422000-25428400	Weak transcription	Small Intestine	intestine
7	chr14:25422200-25424000	Enhancers	Brain Angular Gyrus	brain
8	chr14:25422200-25424200	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr14:25422200-25424400	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr14:25422200-25426400	Enhancers	Left Ventricle	heart
11	chr14:25422200-25427200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr14:25422400-25424000	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr14:25422400-25425000	Enhancers	Right Ventricle	heart
14	chr14:25422600-25424000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr14:25422600-25424200	Enhancers	Fetal Lung	lung
16	chr14:25422600-25426000	Weak transcription	HSMM	muscle
17	chr14:25422600-25426800	Enhancers	GM12878-XiMat	blood
18	chr14:25422600-25428400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr14:25422600-25428400	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr14:25422600-25434000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr14:25422800-25426200	Weak transcription	Aorta	Aorta
22	chr14:25422800-25428400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr14:25423000-25427400	Enhancers	Fetal Heart	heart
24	chr14:25423200-25424000	Enhancers	Colon Smooth Muscle	Colon
25	chr14:25423200-25424800	Enhancers	Stomach Smooth Muscle	stomach
26	chr14:25423200-25425200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr14:25423200-25425200	Enhancers	Lung	lung
28	chr14:25423200-25426200	Enhancers	Fetal Muscle Leg	muscle
29	chr14:25423400-25424200	Enhancers	HepG2	liver
30	chr14:25423400-25425000	Weak transcription	HSMMtube	muscle
31	chr14:25423400-25426000	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr14:25423400-25426800	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr14:25423400-25428000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr14:25423400-25428400	Weak transcription	Adipose Nuclei	Adipose
35	chr14:25423600-25424200	Enhancers	Fetal Kidney	kidney
36	chr14:25423600-25425000	Enhancers	Right Atrium	heart
37	chr14:25423600-25426200	Weak transcription	Brain Anterior Caudate	brain
38	chr14:25423600-25427600	Weak transcription	Brain Substantia Nigra	brain
39	chr14:25423600-25429200	Weak transcription	Placenta	Placenta
40	chr14:25423800-25424400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr14:25423800-25425200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr14:25423800-25427400	Weak transcription	Brain Cingulate Gyrus	brain
43	chr14:25423800-25428200	Weak transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links