Variant report

Variant	rs4594656
Chromosome Location	chr3:142380508-142380509
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	E2F4	chr3:142380466-142380667	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
PLS1-AS1	TF binding region
PLS1	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11917460	1.00[CEU][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11928203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13071750	0.89[CEU][hapmap];0.83[AMR][1000 genomes]
rs13074153	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13078890	0.86[AMR][1000 genomes]
rs13091247	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13095394	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2140437	1.00[CEU][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2354858	1.00[CEU][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34392719	0.89[CEU][hapmap];0.82[AMR][1000 genomes]
rs4683427	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62278480	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6809448	0.85[AMR][1000 genomes]
rs7650047	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932989	chr3:142204208-142423305	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142366000-142435400	Weak transcription	Colonic Mucosa	Colon
2	chr3:142369400-142408400	Weak transcription	Pancreas	Pancrea
3	chr3:142371000-142393800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:142372000-142382000	Weak transcription	HepG2	liver
5	chr3:142372000-142382800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:142372600-142381800	Weak transcription	Fetal Intestine Small	intestine
7	chr3:142372600-142391200	Weak transcription	K562	blood
8	chr3:142376000-142382400	Weak transcription	Duodenum Mucosa	Duodenum
9	chr3:142376200-142382000	Weak transcription	Fetal Intestine Large	intestine
10	chr3:142376400-142381600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr3:142376600-142388800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:142377200-142381600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr3:142378200-142382200	Weak transcription	Stomach Mucosa	stomach
14	chr3:142379200-142413000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:142379400-142380600	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr3:142379400-142382000	Weak transcription	A549	lung
17	chr3:142380000-142382000	Weak transcription	Liver	Liver
18	chr3:142380000-142382600	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr3:142380000-142390000	Weak transcription	Dnd41	blood
20	chr3:142380000-142390400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:142380000-142391800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr3:142380200-142383200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr3:142380200-142383600	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr3:142380200-142388800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr3:142380200-142391000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr3:142380400-142383200	Weak transcription	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links