Variant report

Variant	rs1017647
Chromosome Location	chr4:79176325-79176326
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr4:79176065-79176617	ECC-1	luminal epithelium:	n/a	n/a
2	NFIC	chr4:79176000-79176631	ECC-1	luminal epithelium:	n/a	n/a

Variant related genes	Relation type
FRAS1	TF binding region

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10028072	1.00[ASN][1000 genomes]
rs1017646	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1017648	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1017650	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1017651	1.00[ASN][1000 genomes]
rs11098114	1.00[ASN][1000 genomes]
rs11098131	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11730332	0.81[AFR][1000 genomes]
rs11941234	0.95[ASN][1000 genomes]
rs13118323	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1378237	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1378238	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1454894	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1454895	0.95[ASN][1000 genomes]
rs1454900	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1454901	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1580105	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17003069	0.95[ASN][1000 genomes]
rs17003070	0.95[ASN][1000 genomes]
rs17003071	0.95[ASN][1000 genomes]
rs17003092	1.00[ASN][1000 genomes]
rs17003108	1.00[ASN][1000 genomes]
rs1823921	0.95[ASN][1000 genomes]
rs1840390	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1840393	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1952400	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1999053	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2008587	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2013764	1.00[ASN][1000 genomes]
rs2013770	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2045169	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2124145	1.00[ASN][1000 genomes]
rs2225198	1.00[ASN][1000 genomes]
rs2867014	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28803795	0.82[ASN][1000 genomes]
rs28806931	0.82[ASN][1000 genomes]
rs345503	1.00[ASN][1000 genomes]
rs345506	1.00[ASN][1000 genomes]
rs345528	0.82[ASN][1000 genomes]
rs4269200	0.81[AFR][1000 genomes]
rs4859919	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4859921	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4859922	1.00[ASN][1000 genomes]
rs60544673	0.95[ASN][1000 genomes]
rs60608669	0.82[ASN][1000 genomes]
rs60862246	0.91[ASN][1000 genomes]
rs61283188	1.00[ASN][1000 genomes]
rs62310014	0.81[AFR][1000 genomes]
rs6533564	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6814182	0.84[ASN][1000 genomes]
rs6820900	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6822551	1.00[ASN][1000 genomes]
rs6822773	0.95[ASN][1000 genomes]
rs6846166	1.00[ASN][1000 genomes]
rs6847377	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6850956	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6855457	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72862191	0.95[ASN][1000 genomes]
rs72862196	0.95[ASN][1000 genomes]
rs72864511	0.91[ASN][1000 genomes]
rs72864520	1.00[ASN][1000 genomes]
rs72864521	1.00[ASN][1000 genomes]
rs72864564	1.00[ASN][1000 genomes]
rs72864567	1.00[ASN][1000 genomes]
rs72864571	1.00[ASN][1000 genomes]
rs72864577	1.00[ASN][1000 genomes]
rs72864587	1.00[ASN][1000 genomes]
rs72866312	0.82[ASN][1000 genomes]
rs7438056	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7667670	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs967635	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534024	chr4:78785189-79437403	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv525530	chr4:79024524-79266563	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv1010782	chr4:79057839-79387207	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv829978	chr4:79144453-79291868	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79144600-79179000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:79169200-79186200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr4:79169200-79187400	Weak transcription	HSMMtube	muscle
4	chr4:79169600-79187800	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr4:79169800-79197400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:79169800-79213800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr4:79170400-79186000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr4:79173600-79177800	Strong transcription	HepG2	liver
9	chr4:79173800-79186200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr4:79173800-79187000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr4:79173800-79187400	Weak transcription	Fetal Stomach	stomach
12	chr4:79174200-79178000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr4:79174600-79178400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr4:79174600-79186000	Weak transcription	Fetal Lung	lung
15	chr4:79174600-79197400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr4:79174800-79177400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr4:79174800-79178600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr4:79174800-79214400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr4:79175000-79177000	Weak transcription	Fetal Brain Female	brain
20	chr4:79175000-79179000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr4:79175000-79179200	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr4:79175000-79179800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr4:79175000-79187600	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr4:79175000-79188000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr4:79175200-79176600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr4:79175200-79185800	Weak transcription	Fetal Kidney	kidney
27	chr4:79175400-79179000	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr4:79175400-79179200	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr4:79175400-79179200	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr4:79175600-79176600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr4:79175600-79176600	Strong transcription	Fetal Intestine Large	intestine
32	chr4:79175800-79176600	Strong transcription	H9 Cell Line	embryonic stem cell
33	chr4:79175800-79177400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr4:79176000-79176400	Strong transcription	Left Ventricle	heart
35	chr4:79176000-79176400	Enhancers	Psoas Muscle	Psoas
36	chr4:79176000-79176600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr4:79176000-79176600	Strong transcription	Fetal Intestine Small	intestine
38	chr4:79176000-79176600	Strong transcription	Pancreas	Pancrea
39	chr4:79176200-79176600	Enhancers	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links