Variant report

Variant	rs16852543
Chromosome Location	chr3:142389496-142389497
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:142387225..142389939-chr3:142390380..142394474,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000199319	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11707731	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs11716882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13075800	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13086677	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];0.90[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap]
rs16852464	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2354859	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4627	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap]
rs67594010	0.91[AMR][1000 genomes];0.92[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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16852543	TRPT1	cis	Liver	GTEx
rs16852543	TRPT1	trans	multi-tissue	Pritchard
rs16852543	PLS1	cis	multi-tissue	Pritchard

Chromatin state (count:37 , 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	chr3:142372600-142391200	Weak transcription	K562	blood
5	chr3:142379200-142413000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:142380000-142390000	Weak transcription	Dnd41	blood
7	chr3:142380000-142390400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:142380000-142391800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr3:142380200-142391000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr3:142382600-142400400	Weak transcription	Gastric	stomach
11	chr3:142384400-142411400	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr3:142384600-142392400	Weak transcription	HepG2	liver
13	chr3:142384800-142390400	Weak transcription	Primary hematopoietic stem cells	blood
14	chr3:142384800-142403000	Weak transcription	Liver	Liver
15	chr3:142385200-142391800	Weak transcription	Fetal Intestine Large	intestine
16	chr3:142385800-142391200	Weak transcription	Fetal Intestine Small	intestine
17	chr3:142385800-142415400	Weak transcription	A549	lung
18	chr3:142386400-142411800	Weak transcription	NHEK	skin
19	chr3:142387400-142401800	Weak transcription	Aorta	Aorta
20	chr3:142387400-142404200	Weak transcription	Small Intestine	intestine
21	chr3:142387400-142413400	Weak transcription	Stomach Mucosa	stomach
22	chr3:142388200-142393200	Strong transcription	Duodenum Mucosa	Duodenum
23	chr3:142388200-142393200	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr3:142388800-142389800	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr3:142388800-142390000	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr3:142388800-142390800	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr3:142389000-142389600	Enhancers	H1 Cell Line	embryonic stem cell
28	chr3:142389000-142389600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:142389000-142389800	Enhancers	iPS-20b Cell Line	embryonic stem cell
30	chr3:142389200-142389600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:142389200-142392000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr3:142389200-142412400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr3:142389200-142414800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr3:142389400-142390200	Enhancers	Pancreatic Islets	Pancreatic Islet
35	chr3:142389400-142391600	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr3:142389400-142408800	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr3:142389400-142410000	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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