Variant report

Variant	rs1045247
Chromosome Location	chr1:227182575-227182576
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:227160421..227162343-chr1:227181472..227183178,2	MCF-7	breast:
2	chr1:227129636..227132325-chr1:227181300..227183713,2	K562	blood:

Extended variants
information (count: 54 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10495259	1.00[AFR][1000 genomes]
rs10495271	0.93[CEU][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs10495272	1.00[ASW][hapmap];0.87[CEU][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10916079	0.93[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11583247	1.00[AFR][1000 genomes]
rs11583340	1.00[AFR][1000 genomes]
rs11586575	1.00[AFR][1000 genomes]
rs11586734	1.00[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12117207	0.91[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap]
rs12121729	0.86[AFR][1000 genomes]
rs12122759	1.00[ASW][hapmap];0.93[CEU][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12127665	1.00[AFR][1000 genomes]
rs12128667	1.00[AFR][1000 genomes]
rs12131913	0.93[CEU][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs12133428	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12134379	0.86[AFR][1000 genomes]
rs12136857	1.00[AFR][1000 genomes]
rs12141838	0.86[AFR][1000 genomes]
rs12739480	0.86[CEU][hapmap]
rs12744825	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs12751015	0.93[CEU][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs12752546	0.86[AFR][1000 genomes]
rs12755437	0.93[AFR][1000 genomes]
rs1320495	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs17544956	1.00[AFR][1000 genomes]
rs17545704	0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs17592190	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17601316	0.88[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs17601919	1.00[AFR][1000 genomes]
rs17602169	1.00[AFR][1000 genomes]
rs1892490	0.82[GIH][hapmap]
rs2150874	1.00[AFR][1000 genomes]
rs2154367	0.82[GIH][hapmap]
rs2777834	0.80[CEU][hapmap]
rs2802275	0.82[CEU][hapmap]
rs2802277	0.82[GIH][hapmap]
rs34169114	1.00[AFR][1000 genomes]
rs34556998	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs35817866	1.00[AFR][1000 genomes]
rs3768422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3768431	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3820651	1.00[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4308948	0.93[CEU][hapmap];1.00[YRI][hapmap]
rs61836468	1.00[AFR][1000 genomes]
rs6664330	1.00[AFR][1000 genomes]
rs6674640	1.00[YRI][hapmap]
rs6681959	1.00[AFR][1000 genomes]
rs6695431	1.00[AFR][1000 genomes]
rs6698156	1.00[AFR][1000 genomes]
rs7512871	0.93[CEU][hapmap];1.00[YRI][hapmap]
rs7526822	1.00[ASW][hapmap];0.93[CEU][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs7538237	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1045247	CDC42BPA	cis	lymphoblastoid	seeQTL
rs1045247	ITPKB	cis	lymphoblastoid	seeQTL
rs1045247	CABC1	cis	parietal	SCAN
rs1045247	ITPKB	cis	parietal	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227154400-227294200	Weak transcription	Hela-S3	cervix
2	chr1:227158400-227183000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr1:227163400-227191200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr1:227173400-227183400	Strong transcription	Cortex derived primary cultured neurospheres	brain
5	chr1:227175200-227198400	Weak transcription	A549	lung
6	chr1:227175200-227210200	Weak transcription	HMEC	breast
7	chr1:227175400-227182600	Genic enhancers	Fetal Intestine Small	intestine
8	chr1:227175600-227183200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr1:227175600-227216200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr1:227176000-227190200	Weak transcription	Esophagus	oesophagus
11	chr1:227176000-227191800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr1:227176000-227216400	Weak transcription	NHLF	lung
13	chr1:227176400-227190400	Weak transcription	Osteobl	bone
14	chr1:227176600-227190000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr1:227177200-227188600	Weak transcription	Fetal Lung	lung
16	chr1:227177400-227255200	Weak transcription	Small Intestine	intestine
17	chr1:227178000-227183200	Strong transcription	Fetal Stomach	stomach
18	chr1:227178200-227183000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:227178200-227188600	Weak transcription	HSMMtube	muscle
20	chr1:227178400-227190400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:227178400-227271200	Weak transcription	Psoas Muscle	Psoas
22	chr1:227178600-227206600	Weak transcription	Primary hematopoietic stem cells	blood
23	chr1:227178600-227226200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr1:227178800-227183000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr1:227178800-227188800	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr1:227179000-227182800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:227179000-227188400	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr1:227179400-227183000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr1:227179400-227183200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr1:227179400-227188200	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr1:227179400-227198400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:227179400-227204400	Weak transcription	Stomach Mucosa	stomach
33	chr1:227179400-227215000	Weak transcription	Placenta	Placenta
34	chr1:227179600-227213800	Weak transcription	NH-A	brain
35	chr1:227180000-227182600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr1:227180000-227183200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:227180200-227183200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr1:227180200-227184200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr1:227180400-227182600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:227180400-227183000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr1:227180400-227184600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr1:227180600-227182600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr1:227180600-227183000	Strong transcription	Liver	Liver
44	chr1:227180600-227183200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr1:227180600-227183200	Strong transcription	Pancreas	Pancrea
46	chr1:227180800-227183200	Strong transcription	Duodenum Mucosa	Duodenum
47	chr1:227180800-227187800	Weak transcription	HSMM	muscle
48	chr1:227180800-227190200	Weak transcription	K562	blood
49	chr1:227181000-227183000	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr1:227181200-227182600	Enhancers	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links