Variant report

Variant	rs3734854
Chromosome Location	chr6:31078836-31078837
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	CTCF	chr6:31078820-31078970	Caco-2	colon:	n/a	n/a
2	CTCF	chr6:31078820-31078970	HEK293	kidney:	n/a	n/a
3	RAD21	chr6:31078626-31079253	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr6:31078771-31078947	HepG2	liver:	n/a	n/a
5	ELF1	chr6:31078608-31078897	GM12878	blood:	n/a	n/a
6	CTCF	chr6:31078787-31078948	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr6:31078800-31078950	WERI-Rb-1	eye:	n/a	n/a
8	RAD21	chr6:31078779-31079038	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr6:31078780-31078930	WERI-Rb-1	eye:	n/a	n/a

Variant related genes	Relation type
PSORS1C1	TF binding region

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10947134	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10947135	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12527394	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12529288	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12662091	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2233963	0.89[AMR][1000 genomes]
rs2233970	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2233972	0.93[AMR][1000 genomes]
rs2233973	0.99[ASN][1000 genomes]
rs2233983	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2233984	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2233985	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517473	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2894179	0.84[ASN][1000 genomes]
rs34209658	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35802713	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4495304	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4713431	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4947246	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4947296	0.96[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4947297	0.96[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4947299	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4947302	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9263460	0.80[ASN][1000 genomes]
rs9263477	0.80[ASN][1000 genomes]
rs9263499	0.85[ASN][1000 genomes]
rs9263512	0.84[ASN][1000 genomes]
rs9263572	0.87[ASN][1000 genomes]
rs9263578	0.87[ASN][1000 genomes]
rs9295949	0.81[ASN][1000 genomes]
rs9295950	0.81[ASN][1000 genomes]
rs9348854	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9357108	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9378152	0.82[AMR][1000 genomes]
rs9380215	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9380217	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9391708	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9391709	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9394037	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9394038	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9404978	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9405049	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	nsv1029442	chr6:31006647-31449207	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	diseases
7	nsv427750	chr6:31028290-31234581	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
8	nsv428140	chr6:31028290-31462106	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	89 gene(s)	inside rSNPs	diseases
9	esv2758042	chr6:31028290-31497106	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	101 gene(s)	inside rSNPs	diseases
10	esv2759414	chr6:31028290-31542308	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	151 gene(s)	inside rSNPs	diseases
11	nsv462746	chr6:31060162-31082361	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
12	nsv601489	chr6:31060162-31082361	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
13	nsv1033227	chr6:31071547-31101674	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31076800-31082200	Weak transcription	Spleen	Spleen
2	chr6:31077400-31081200	Weak transcription	Right Atrium	heart
3	chr6:31077600-31079200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
4	chr6:31077600-31080400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:31077600-31082600	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr6:31077800-31079600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
7	chr6:31077800-31080400	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr6:31077800-31080600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:31078000-31079200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr6:31078200-31079000	Enhancers	H1 Cell Line	embryonic stem cell
11	chr6:31078200-31079200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
12	chr6:31078200-31079400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr6:31078200-31079600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
14	chr6:31078200-31082200	Weak transcription	Gastric	stomach
15	chr6:31078400-31079200	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr6:31078600-31081200	Weak transcription	Stomach Mucosa	stomach
17	chr6:31078800-31079000	Enhancers	Placenta Amnion	Placenta Amnion
18	chr6:31078800-31080000	Enhancers	HSMM	muscle
19	chr6:31078800-31081200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr6:31078800-31082200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:31078800-31082200	Weak transcription	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links