Variant report

Variant	rs4430277
Chromosome Location	chr1:153493615-153493616
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:153491196..153497339-chr1:153538209..153542553,6	MCF-7	breast:
2	chr1:153492067..153494690-chr1:153506772..153509509,2	MCF-7	breast:
3	chr1:153488431..153490031-chr1:153491470..153493737,3	MCF-7	breast:
4	chr1:153492157..153493956-chr1:153538151..153541270,3	MCF-7	breast:
5	chr1:153492181..153495094-chr1:153498850..153501392,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196754	Chromatin interaction
ENSG00000197956	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs16835366	0.86[GIH][hapmap];0.90[JPT][hapmap]
rs16835368	0.85[GIH][hapmap];0.90[JPT][hapmap]
rs16835382	1.00[JPT][hapmap]
rs16835393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17695220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1887039	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2094217	0.94[EUR][1000 genomes]
rs2094737	0.94[EUR][1000 genomes]
rs2094738	0.96[EUR][1000 genomes]
rs2248745	0.81[EUR][1000 genomes]
rs2262587	0.94[EUR][1000 genomes]
rs2339696	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2480695	0.92[CEU][hapmap];0.86[GIH][hapmap]
rs28410699	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28464843	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28483109	0.92[CEU][hapmap];0.86[GIH][hapmap];0.82[MEX][hapmap]
rs28632016	0.83[ASN][1000 genomes]
rs28635377	0.83[ASN][1000 genomes]
rs2879553	0.90[JPT][hapmap]
rs3762262	0.81[EUR][1000 genomes]
rs4017737	0.92[CEU][hapmap];0.86[GIH][hapmap]
rs4272569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs477339	0.92[CEU][hapmap]
rs4845351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4845352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845549	0.86[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs4845550	1.00[JPT][hapmap]
rs4845552	0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[ASN][1000 genomes]
rs4845553	0.83[ASN][1000 genomes]
rs4845554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4845555	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs532652	0.92[CEU][hapmap];0.88[CHB][hapmap];0.92[GIH][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs550597	0.92[CEU][hapmap];0.86[GIH][hapmap]
rs552446	0.81[EUR][1000 genomes]
rs585215	0.85[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap]
rs6587743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6587745	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6587746	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs659403	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs6659755	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6672390	0.86[GIH][hapmap];0.90[JPT][hapmap]
rs6684970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6690638	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6690712	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7515940	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7518306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7520093	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7534343	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7534347	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7534830	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7537898	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7544359	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9426945	0.94[EUR][1000 genomes]
rs9427239	0.92[CEU][hapmap];0.88[CHB][hapmap];0.92[GIH][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs9427287	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9436095	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv1002705	chr1:153307852-153525589	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	nsv831603	chr1:153405842-153576143	Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	148 gene(s)	inside rSNPs	diseases
5	nsv1007306	chr1:153413827-153541798	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	146 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4430277	SPRR4	cis	parietal	SCAN
rs4430277	GBA	cis	parietal	SCAN
rs4430277	TDRD10	cis	cerebellum	SCAN
rs4430277	PSMB4	cis	parietal	SCAN
rs4430277	PKLR	cis	parietal	SCAN
rs4430277	KIAA0513	trans	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153481200-153503600	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr1:153483800-153497800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr1:153488600-153498200	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr1:153488800-153497800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:153489000-153497800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:153489000-153497800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:153489000-153498000	Weak transcription	Esophagus	oesophagus
8	chr1:153489000-153498000	Weak transcription	Fetal Muscle Trunk	muscle
9	chr1:153489000-153506000	Weak transcription	Gastric	stomach
10	chr1:153489400-153498200	Weak transcription	Hela-S3	cervix
11	chr1:153491400-153495200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:153491800-153498400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:153492000-153494200	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr1:153492000-153494200	Enhancers	Fetal Intestine Large	intestine
15	chr1:153492000-153499200	Weak transcription	Fetal Thymus	thymus
16	chr1:153492200-153495000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:153492400-153495000	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr1:153492400-153498400	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr1:153492800-153493800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
20	chr1:153492800-153493800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:153492800-153493800	Enhancers	Placenta	Placenta
22	chr1:153492800-153494000	Enhancers	Fetal Intestine Small	intestine
23	chr1:153492800-153494000	Enhancers	Rectal Mucosa Donor 29	rectum
24	chr1:153492800-153494000	Enhancers	Stomach Mucosa	stomach
25	chr1:153492800-153494000	Enhancers	HMEC	breast
26	chr1:153493000-153493800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
27	chr1:153493000-153493800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
28	chr1:153493000-153494000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:153493000-153499400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr1:153493200-153493800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
31	chr1:153493200-153493800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr1:153493200-153493800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:153493200-153494000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:153493200-153494000	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr1:153493400-153493800	Enhancers	NHEK	skin
36	chr1:153493400-153494000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:153493400-153494000	Enhancers	Duodenum Mucosa	Duodenum
38	chr1:153493600-153494000	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr1:153493600-153495200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr1:153493600-153497800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr1:153493600-153497800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr1:153493600-153497800	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr1:153493600-153497800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr1:153493600-153497800	Weak transcription	K562	blood
45	chr1:153493600-153498000	Weak transcription	Pancreas	Pancrea
46	chr1:153493600-153504000	Weak transcription	Colonic Mucosa	Colon

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