Variant report

Variant	rs10178804
Chromosome Location	chr2:36597085-36597086
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:36581462..36584625-chr2:36596620..36599809,5	MCF-7	breast:
2	chr2:36582124..36584781-chr2:36595194..36598033,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000150938	Chromatin interaction
ENSG00000260025	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10167894	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10186135	1.00[CHB][hapmap]
rs10192912	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10198159	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10203010	1.00[CHB][hapmap]
rs11124514	1.00[CHB][hapmap]
rs11124515	1.00[CHB][hapmap]
rs1159133	1.00[CHB][hapmap]
rs11885395	1.00[ASN][1000 genomes]
rs11898050	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12465282	1.00[CHB][hapmap]
rs12465297	1.00[CHB][hapmap]
rs12477836	1.00[CHB][hapmap]
rs12712500	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13394052	1.00[CHB][hapmap]
rs13407488	1.00[CHB][hapmap]
rs17480064	1.00[ASN][1000 genomes]
rs3755214	1.00[CHB][hapmap]
rs3770932	1.00[CHB][hapmap]
rs3770936	1.00[CHB][hapmap]
rs4233914	1.00[CHB][hapmap]
rs4670144	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4670545	1.00[ASN][1000 genomes]
rs4670547	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4670554	1.00[CHB][hapmap]
rs55653640	1.00[ASN][1000 genomes]
rs6711707	1.00[CHB][hapmap]
rs7589917	1.00[CHB][hapmap]
rs9308991	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9308992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs997602	1.00[CHB][hapmap];1.00[ASN][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	nsv833803	chr2:36589065-36745779	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10178804	QPCT	cis	parietal	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:36586200-36603600	Weak transcription	Brain Germinal Matrix	brain
2	chr2:36586200-36626600	Weak transcription	Primary B cells from cord blood	blood
3	chr2:36590000-36598200	Genic enhancers	Muscle Satellite Cultured Cells	--
4	chr2:36590800-36597200	Enhancers	H1 Cell Line	embryonic stem cell
5	chr2:36592400-36599800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:36592400-36605800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:36592600-36597200	Enhancers	Placenta Amnion	Placenta Amnion
8	chr2:36592600-36597200	Enhancers	Right Atrium	heart
9	chr2:36592800-36598200	Enhancers	NHDF-Ad	bronchial
10	chr2:36593200-36598000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:36593200-36598000	Genic enhancers	HSMM	muscle
12	chr2:36593400-36599400	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr2:36593400-36601800	Enhancers	Fetal Lung	lung
14	chr2:36593600-36597200	Enhancers	H9 Cell Line	embryonic stem cell
15	chr2:36593600-36598400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:36593600-36602400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr2:36593800-36598400	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr2:36594000-36603600	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr2:36594200-36601600	Weak transcription	Fetal Brain Male	brain
20	chr2:36594200-36605400	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr2:36594400-36602000	Enhancers	Fetal Heart	heart
22	chr2:36594600-36597200	Enhancers	Psoas Muscle	Psoas
23	chr2:36594600-36597200	Enhancers	Right Ventricle	heart
24	chr2:36594800-36597200	Enhancers	Ovary	ovary
25	chr2:36594800-36597200	Transcr. at gene 5' and 3'	A549	lung
26	chr2:36594800-36597600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr2:36595000-36597200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:36595200-36597200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:36595200-36606000	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr2:36595400-36597400	Genic enhancers	HUVEC	blood vessel
31	chr2:36595400-36598200	Enhancers	Stomach Smooth Muscle	stomach
32	chr2:36595400-36599800	Weak transcription	Gastric	stomach
33	chr2:36595400-36600200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr2:36595400-36603600	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr2:36595600-36598200	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr2:36595600-36598200	Enhancers	Adipose Nuclei	Adipose
37	chr2:36595600-36598200	Weak transcription	Colonic Mucosa	Colon
38	chr2:36595600-36598200	Weak transcription	Esophagus	oesophagus
39	chr2:36595600-36598200	Enhancers	Hela-S3	cervix
40	chr2:36595600-36598400	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr2:36595600-36598400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr2:36595600-36598400	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr2:36595600-36600600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr2:36595600-36604200	Weak transcription	Fetal Muscle Trunk	muscle
45	chr2:36595600-36604400	Enhancers	Colon Smooth Muscle	Colon
46	chr2:36595800-36598000	Weak transcription	Duodenum Mucosa	Duodenum
47	chr2:36595800-36598000	Weak transcription	Fetal Intestine Large	intestine
48	chr2:36596000-36597200	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
49	chr2:36596000-36597200	Genic enhancers	HMEC	breast
50	chr2:36596000-36597600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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