Variant report

Variant	rs1887039
Chromosome Location	chr1:153488723-153488724
allele	C/T
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:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153488074..153490383-chr1:153582465..153584577,2	MCF-7	breast:
2	chr1:153488456..153491152-chr1:153500196..153502080,2	MCF-7	breast:
3	chr1:153487137..153489492-chr1:153599927..153602153,2	K562	blood:
4	chr1:153482943..153489100-chr1:153536653..153546582,24	MCF-7	breast:
5	chr1:153488592..153490100-chr1:153698807..153700904,2	MCF-7	breast:
6	chr1:153488431..153490031-chr1:153491470..153493737,3	MCF-7	breast:
7	chr1:153480132..153490926-chr1:153537975..153544732,26	MCF-7	breast:
8	chr1:153485568..153489846-chr1:153597780..153600586,4	MCF-7	breast:
9	chr1:153333970..153336324-chr1:153487147..153490000,2	MCF-7	breast:
10	chr1:153482414..153491614-chr1:153504332..153509728,11	MCF-7	breast:
11	chr1:153485492..153490407-chr1:153581456..153585636,6	MCF-7	breast:
12	chr1:153486911..153489748-chr1:153497891..153499485,2	MCF-7	breast:
13	chr1:153487607..153489712-chr1:153493961..153496551,2	MCF-7	breast:
14	chr1:153481535..153486377-chr1:153486910..153489741,6	MCF-7	breast:
15	chr1:153486453..153490659-chr1:153516922..153519172,4	MCF-7	breast:
16	chr1:153488382..153488936-chr20:48729328..48730006,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
ENSG00000196754	Chromatin interaction
ENSG00000160678	Chromatin interaction
ENSG00000196154	Chromatin interaction
ENSG00000197956	Chromatin interaction
ENSG00000189171	Chromatin interaction
ENSG00000244687	Chromatin interaction
ENSG00000143624	Chromatin interaction
ENSG00000188643	Chromatin interaction
ENSG00000199565	Chromatin interaction
ENSG00000238279	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs16835366	0.86[GIH][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs16835368	0.85[GIH][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs16835382	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
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];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1964151	0.85[ASN][1000 genomes]
rs2094217	0.86[EUR][1000 genomes]
rs2094737	0.86[EUR][1000 genomes]
rs2094738	0.87[EUR][1000 genomes]
rs2262587	0.86[EUR][1000 genomes]
rs2339696	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2480695	0.92[CEU][hapmap];0.86[GIH][hapmap]
rs28410699	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28464843	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28483109	0.92[CEU][hapmap];0.86[GIH][hapmap];0.82[MEX][hapmap]
rs28632016	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs28635377	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs28676601	0.82[ASN][1000 genomes]
rs28707433	0.82[ASN][1000 genomes]
rs2879553	0.90[JPT][hapmap]
rs3762262	0.80[AMR][1000 genomes]
rs3915524	0.85[ASN][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];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4430277	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]
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];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4845352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4845548	0.82[ASN][1000 genomes]
rs4845549	0.86[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4845550	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4845551	0.85[ASN][1000 genomes]
rs4845552	0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4845553	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4845554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845555	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs532652	0.92[CEU][hapmap];0.88[CHB][hapmap];0.92[GIH][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs550597	0.92[CEU][hapmap];0.86[GIH][hapmap]
rs552446	0.80[AMR][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];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6587745	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6587746	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs659403	0.91[CEU][hapmap];0.80[AMR][1000 genomes]
rs6659755	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6660055	0.82[ASN][1000 genomes]
rs6672390	0.86[GIH][hapmap];0.90[JPT][hapmap]
rs6679509	0.82[ASN][1000 genomes]
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];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6690638	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6690712	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696893	0.86[ASN][1000 genomes]
rs7515940	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7520093	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7534343	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7534347	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7534823	0.83[ASN][1000 genomes]
rs7534830	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7537898	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7544359	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9426945	0.86[EUR][1000 genomes]
rs9427239	0.92[CEU][hapmap];0.88[CHB][hapmap];0.92[GIH][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs9427287	0.86[EUR][1000 genomes]
rs9436094	0.82[ASN][1000 genomes]
rs9436095	0.82[AMR][1000 genomes];0.89[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	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
6	nsv946400	chr1:153488627-153492093	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer	Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1887039	SPRR4	cis	parietal	SCAN
rs1887039	TDRD10	cis	cerebellum	SCAN
rs1887039	PSMB4	cis	parietal	SCAN
rs1887039	PKLR	cis	parietal	SCAN
rs1887039	KIAA0513	trans	parietal	SCAN
rs1887039	GBA	cis	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153481000-153490600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr1:153481200-153503600	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr1:153483600-153488800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr1:153483600-153493200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:153483800-153497800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:153485600-153489000	Enhancers	Primary B cells from cord blood	blood
7	chr1:153486400-153489400	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr1:153486800-153489600	Enhancers	Placenta	Placenta
9	chr1:153487000-153488800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
10	chr1:153487200-153488800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:153487200-153489000	Enhancers	Esophagus	oesophagus
12	chr1:153487200-153489000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr1:153487600-153488800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:153487600-153489000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:153487600-153489000	Enhancers	Placenta Amnion	Placenta Amnion
16	chr1:153487600-153489400	Enhancers	Stomach Mucosa	stomach
17	chr1:153487800-153488800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr1:153487800-153488800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:153487800-153488800	Enhancers	A549	lung
20	chr1:153487800-153489000	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr1:153487800-153489000	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr1:153487800-153489000	Enhancers	Colonic Mucosa	Colon
23	chr1:153487800-153489400	Enhancers	Fetal Intestine Large	intestine
24	chr1:153488000-153488800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:153488000-153488800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr1:153488000-153488800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:153488000-153488800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
28	chr1:153488000-153488800	Enhancers	Right Atrium	heart
29	chr1:153488000-153488800	Enhancers	Right Ventricle	heart
30	chr1:153488000-153488800	Enhancers	Spleen	Spleen
31	chr1:153488000-153488800	Flanking Active TSS	NHEK	skin
32	chr1:153488000-153489000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:153488000-153489000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:153488000-153489000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr1:153488000-153489000	Enhancers	Fetal Muscle Trunk	muscle
36	chr1:153488000-153489000	Enhancers	Gastric	stomach
37	chr1:153488000-153489000	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr1:153488000-153489200	Enhancers	Fetal Intestine Small	intestine
39	chr1:153488000-153489200	Flanking Active TSS	Hela-S3	cervix
40	chr1:153488200-153488800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:153488200-153488800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:153488200-153488800	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr1:153488200-153489000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr1:153488200-153489000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
45	chr1:153488200-153490400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr1:153488400-153489200	Weak transcription	Small Intestine	intestine
47	chr1:153488400-153489400	Enhancers	Rectal Mucosa Donor 29	rectum
48	chr1:153488400-153489400	Enhancers	HMEC	breast
49	chr1:153488400-153490400	Weak transcription	Primary hematopoietic stem cells	blood
50	chr1:153488400-153492400	Enhancers	Primary monocytes fromperipheralblood	blood

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