Variant report

Variant	rs10788803
Chromosome Location	chr1:151263782-151263783
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151262262..151263961-chr1:151340397..151342211,2	MCF-7	breast:
2	chr1:151260960..151263858-chr1:151273535..151276289,2	K562	blood:
3	chr1:151262059..151264776-chr1:151727556..151730221,2	K562	blood:
4	chr1:151261557..151264392-chr1:151278730..151281200,2	K562	blood:
5	1:151254384-151268403..1:151402394-151411623	GM12878	blood:
6	chr1:151238343..151240219-chr1:151263563..151265288,2	MCF-7	breast:
7	chr1:151263384..151266874-chr1:151371914..151374890,3	MCF-7	breast:
8	chr1:151262712..151264212-chr13:108866472..108868274,2	K562	blood:
9	chr1:151263503..151265066-chr1:151300578..151302446,2	MCF-7	breast:
10	1:151171193-151178589..1:151254384-151268403	Hela-S3	cervix:
11	chr1:151160872..151162663-chr1:151262969..151264580,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000159352	Chromatin interaction
ENSG00000163159	Chromatin interaction
ENSG00000143398	Chromatin interaction
ENSG00000269621	Chromatin interaction
ENSG00000174405	Chromatin interaction
ENSG00000143416	Chromatin interaction
ENSG00000143393	Chromatin interaction
ENSG00000236940	Chromatin interaction
ENSG00000159377	Chromatin interaction
ENSG00000238711	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1056847	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10749660	0.85[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs10788801	0.86[JPT][hapmap]
rs10788804	0.96[CEU][hapmap];0.83[GIH][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap]
rs10888408	0.90[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10888409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10888410	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10888411	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11204785	0.80[CHD][hapmap];0.95[JPT][hapmap]
rs11204791	0.85[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11204795	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12048670	0.90[ASN][1000 genomes]
rs12062719	0.80[ASN][1000 genomes]
rs12407426	0.82[ASN][1000 genomes]
rs1536617	0.91[JPT][hapmap]
rs16827941	0.83[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs16833079	0.80[ASN][1000 genomes]
rs1752387	0.85[JPT][hapmap]
rs1892196	0.90[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs2025900	0.82[JPT][hapmap]
rs2031797	0.84[GIH][hapmap];0.91[JPT][hapmap]
rs2275900	0.85[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2769268	0.82[JPT][hapmap]
rs2769273	0.82[JPT][hapmap]
rs2800946	0.82[JPT][hapmap]
rs3811405	0.86[JPT][hapmap]
rs3811406	0.86[GIH][hapmap];0.91[JPT][hapmap]
rs41302131	0.89[ASN][1000 genomes]
rs4246525	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4520422	0.84[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs4522000	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4636463	0.90[JPT][hapmap]
rs4970944	0.80[CHD][hapmap];0.95[JPT][hapmap]
rs4970948	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4971013	0.85[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs4971016	0.81[ASN][1000 genomes]
rs4971021	0.81[ASN][1000 genomes]
rs4971023	0.85[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs4971025	0.89[ASN][1000 genomes]
rs4971026	0.89[ASN][1000 genomes]
rs4971027	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4971029	0.91[JPT][hapmap]
rs4971030	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4971031	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4971032	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4971033	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs5022636	0.88[CEU][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6587559	0.85[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.82[ASN][1000 genomes]
rs6587562	0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[ASN][1000 genomes]
rs6678528	0.86[JPT][hapmap]
rs6681071	0.88[ASN][1000 genomes]
rs6681163	0.88[ASN][1000 genomes]
rs6686402	0.85[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.82[ASN][1000 genomes]
rs6695344	0.85[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap]
rs6701325	0.82[ASN][1000 genomes]
rs744536	0.81[ASW][hapmap];0.92[CEU][hapmap];0.83[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap]
rs7518924	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7527032	0.85[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.82[ASN][1000 genomes]
rs7532935	0.85[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.82[ASN][1000 genomes]
rs7539584	0.85[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs7544947	0.85[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.82[ASN][1000 genomes]
rs7545392	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7552906	1.00[CEU][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs943637	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
2	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
3	nsv831570	chr1:151129020-151281778	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
4	esv2754960	chr1:151240542-151331304	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
5	esv34461	chr1:151240542-151411635	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
6	esv2753774	chr1:151240542-151411635	Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10788803	SELENBP1	cis	cerebellum	SCAN
rs10788803	PSMD4	cis	cerebellum	SCAN
rs10788803	PSMD4	cis	parietal	SCAN
rs10788803	HIST2H2AC	cis	parietal	SCAN
rs10788803	CTSS	cis	cerebellum	SCAN
rs10788803	LCE5A	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151256000-151270600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:151256800-151264600	Weak transcription	NHDF-Ad	bronchial
3	chr1:151256800-151268400	Strong transcription	NHEK	skin
4	chr1:151256800-151281400	Strong transcription	Fetal Stomach	stomach
5	chr1:151257000-151266400	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr1:151257000-151266600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:151257000-151266600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr1:151257000-151267000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:151257000-151281200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:151257000-151281800	Weak transcription	Right Atrium	heart
11	chr1:151257200-151266000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:151257200-151266400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
13	chr1:151257200-151270200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr1:151257200-151283000	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr1:151257200-151297600	Strong transcription	Dnd41	blood
16	chr1:151257400-151264000	Strong transcription	H9 Cell Line	embryonic stem cell
17	chr1:151257400-151265000	Strong transcription	Fetal Thymus	thymus
18	chr1:151257400-151265800	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr1:151257400-151266400	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr1:151257400-151266400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr1:151257400-151267400	Weak transcription	Fetal Brain Male	brain
22	chr1:151257400-151272200	Strong transcription	HepG2	liver
23	chr1:151257400-151281200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:151257400-151281200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:151257400-151281800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:151257400-151282000	Strong transcription	Fetal Lung	lung
27	chr1:151257400-151282200	Strong transcription	Fetal Intestine Large	intestine
28	chr1:151257400-151282200	Strong transcription	Osteobl	bone
29	chr1:151257400-151283600	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr1:151257600-151264400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr1:151257600-151264800	Strong transcription	Fetal Muscle Leg	muscle
32	chr1:151257600-151266400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr1:151257600-151270800	Weak transcription	Fetal Heart	heart
34	chr1:151257600-151272200	Strong transcription	Primary T cells from cord blood	blood
35	chr1:151257600-151281200	Strong transcription	Adipose Nuclei	Adipose
36	chr1:151257600-151281200	Strong transcription	Skeletal Muscle Male	skeletal muscle
37	chr1:151257600-151293600	Strong transcription	Brain Germinal Matrix	brain
38	chr1:151257800-151265000	Strong transcription	Primary B cells from cord blood	blood
39	chr1:151257800-151266800	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr1:151257800-151269000	Strong transcription	GM12878-XiMat	blood
41	chr1:151257800-151281600	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr1:151257800-151282000	Strong transcription	Duodenum Mucosa	Duodenum
43	chr1:151258000-151283200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr1:151258000-151283600	Strong transcription	Lung	lung
45	chr1:151258200-151266800	Strong transcription	Brain Angular Gyrus	brain
46	chr1:151258200-151266800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr1:151258200-151271800	Strong transcription	Primary hematopoietic stem cells	blood
48	chr1:151258200-151271800	Strong transcription	Gastric	stomach
49	chr1:151258200-151281400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:151258200-151281600	Strong transcription	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links