Variant report

Variant	rs342078
Chromosome Location	chr2:20702315-20702316
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr2:20701838-20702327	SK-N-SH	brain:	n/a	n/a
2	MAX	chr2:20701789-20702670	Hela-S3	cervix:	n/a	n/a
3	CEBPB	chr2:20701793-20702637	Hela-S3	cervix:	n/a	n/a
4	GATA3	chr2:20701849-20702339	SK-N-SH	brain:	n/a	n/a
5	GTF3C2	chr2:20702250-20702769	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr2:20701843-20702677	MCF10A-Er-Src	breast:	n/a	n/a
7	RPC155	chr2:20701795-20702645	Hela-S3	cervix:	n/a	n/a
8	CEBPB	chr2:20701874-20702346	A549	lung:	n/a	n/a
9	TCF7L2	chr2:20701854-20702539	Hela-S3	cervix:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:20701817..20704482-chr2:20832644..20835192,2	MCF-7	breast:
2	chr2:20673127..20675956-chr2:20701359..20706220,5	MCF-7	breast:
3	chr2:20702007..20704180-chr2:20704465..20706465,2	MCF-7	breast:
4	chr2:20645810..20649002-chr2:20701951..20704160,3	MCF-7	breast:
5	chr2:20645423..20650748-chr2:20698837..20705480,9	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000227047	TF binding region
ENSG00000143878	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs342075	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs342135	0.83[ASN][1000 genomes]
rs342136	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs896734	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873717	chr2:20625174-20756900	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv873718	chr2:20627875-20752152	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv873719	chr2:20628882-20756900	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
4	nsv833537	chr2:20630092-20826816	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
5	nsv873720	chr2:20645835-20756900	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv873721	chr2:20645835-20759789	Enhancers Bivalent Enhancer Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
7	nsv873722	chr2:20652507-20705910	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv873723	chr2:20678000-20720237	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv873724	chr2:20678000-20757286	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv833548	chr2:20682073-20864078	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20692400-20715200	Weak transcription	Right Atrium	heart
2	chr2:20696800-20705600	Weak transcription	NHLF	lung
3	chr2:20697000-20705600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr2:20697000-20706200	Weak transcription	Left Ventricle	heart
5	chr2:20697000-20714000	Weak transcription	Right Ventricle	heart
6	chr2:20697200-20714200	Weak transcription	HSMMtube	muscle
7	chr2:20697800-20706200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr2:20698800-20702600	Enhancers	Placenta	Placenta
9	chr2:20699400-20702400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr2:20700600-20702600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr2:20700600-20702800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:20700800-20702600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:20701000-20703600	Weak transcription	NHEK	skin
14	chr2:20701000-20705600	Weak transcription	Osteobl	bone
15	chr2:20701000-20705800	Weak transcription	HSMM	muscle
16	chr2:20701000-20705800	Weak transcription	NHDF-Ad	bronchial
17	chr2:20701000-20706000	Weak transcription	NH-A	brain
18	chr2:20701200-20705600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:20701200-20706000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:20701200-20706000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr2:20701200-20709000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:20701400-20706600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:20701800-20702600	Enhancers	A549	lung
24	chr2:20701800-20705600	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr2:20701800-20705600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr2:20701800-20706000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:20701800-20709000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:20702000-20703800	Weak transcription	HepG2	liver
29	chr2:20702200-20702600	Flanking Active TSS	Hela-S3	cervix
30	chr2:20702200-20706200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links