Variant report

Variant	rs6587743
Chromosome Location	chr1:153481717-153481718
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	chr1:153481535..153486377-chr1:153486910..153489741,6	MCF-7	breast:
2	chr1:153480033..153483904-chr1:153604458..153606849,3	K562	blood:
3	chr1:153479765..153482193-chr1:153627799..153629535,2	K562	blood:
4	chr1:153327311..153331799-chr1:153480650..153484791,7	MCF-7	breast:
5	chr1:153480481..153484963-chr1:153582556..153586017,6	MCF-7	breast:
6	chr1:153480132..153490926-chr1:153537975..153544732,26	MCF-7	breast:
7	chr1:153478376..153480788-chr1:153481314..153483652,2	K562	blood:
8	chr1:153480135..153482234-chr1:153578835..153581505,2	MCF-7	breast:
9	chr1:153480765..153482586-chr1:153640638..153643448,2	MCF-7	breast:
10	chr1:153320974..153341807-chr1:153456098..153486349,81	MCF-7	breast:
11	chr1:153479337..153482179-chr1:153578655..153582224,3	MCF-7	breast:
12	chr1:153480409..153482467-chr1:153599959..153601900,2	MCF-7	breast:
13	chr1:153341060..153343420-chr1:153479644..153482399,2	MCF-7	breast:
14	chr1:153480699..153483560-chr1:153583729..153585573,2	MCF-7	breast:
15	chr1:153479500..153482310-chr1:153538620..153542576,5	MCF-7	breast:
16	chr1:153476869..153479043-chr1:153480773..153483334,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000163220	Chromatin interaction
ENSG00000272030	Chromatin interaction
ENSG00000196754	Chromatin interaction
ENSG00000163218	Chromatin interaction
ENSG00000188643	Chromatin interaction
ENSG00000160679	Chromatin interaction
ENSG00000160678	Chromatin interaction
ENSG00000143621	Chromatin interaction
ENSG00000189171	Chromatin interaction
ENSG00000271853	Chromatin interaction

Extended variants
information (count: 71 )
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];0.85[ASN][1000 genomes]
rs16835368	0.85[GIH][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs16835382	1.00[JPT][hapmap];0.88[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];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17695220	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1887039	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	0.88[ASN][1000 genomes]
rs2094217	0.84[EUR][1000 genomes]
rs2094737	0.84[EUR][1000 genomes]
rs2094738	0.86[EUR][1000 genomes]
rs2248745	0.83[AMR][1000 genomes]
rs2262587	0.84[EUR][1000 genomes]
rs2339696	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2480695	0.92[CEU][hapmap];0.86[GIH][hapmap]
rs28410699	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28464843	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28483109	0.92[CEU][hapmap];0.86[GIH][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes]
rs28632016	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28635377	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28676601	0.85[ASN][1000 genomes]
rs28707433	0.85[ASN][1000 genomes]
rs2879553	0.90[JPT][hapmap]
rs3762262	0.86[AMR][1000 genomes]
rs3915524	0.88[ASN][1000 genomes]
rs4017737	0.92[CEU][hapmap];0.86[GIH][hapmap];0.83[AMR][1000 genomes]
rs4272569	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4430277	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]
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];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4845352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4845548	0.85[ASN][1000 genomes]
rs4845549	0.86[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4845550	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4845551	0.88[ASN][1000 genomes]
rs4845552	0.91[ASW][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.82[MEX][hapmap];0.95[MKK][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4845553	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4845554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4845555	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs532652	0.92[CEU][hapmap];0.88[CHB][hapmap];0.92[GIH][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs550597	0.92[CEU][hapmap];0.86[GIH][hapmap]
rs552446	0.86[AMR][1000 genomes]
rs585215	0.85[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs6587745	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587746	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs659403	0.91[CEU][hapmap];0.86[AMR][1000 genomes]
rs6659755	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6660055	0.85[ASN][1000 genomes]
rs6672390	0.86[GIH][hapmap];0.90[JPT][hapmap]
rs6679509	0.85[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];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6690638	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6690712	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6696893	0.89[ASN][1000 genomes]
rs7515940	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[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];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7520093	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7534343	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7534347	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7534830	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7537898	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7544359	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9426945	0.84[EUR][1000 genomes]
rs9427239	0.92[CEU][hapmap];0.88[CHB][hapmap];0.92[GIH][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs9427287	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9436094	0.85[ASN][1000 genomes]
rs9436095	0.82[AMR][1000 genomes];0.93[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
rs6587743	PSMB4	cis	parietal	SCAN
rs6587743	TDRD10	cis	cerebellum	SCAN
rs6587743	GBA	cis	parietal	SCAN
rs6587743	PKLR	cis	parietal	SCAN
rs6587743	KIAA0513	trans	parietal	SCAN
rs6587743	SPRR4	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153478000-153482200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:153478000-153482600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr1:153478800-153482200	Enhancers	NHEK	skin
4	chr1:153478800-153482400	Enhancers	HMEC	breast
5	chr1:153479200-153482000	Weak transcription	Spleen	Spleen
6	chr1:153479200-153485200	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr1:153479200-153487600	Weak transcription	Small Intestine	intestine
8	chr1:153479600-153483400	Weak transcription	K562	blood
9	chr1:153479800-153482200	Weak transcription	Pancreas	Pancrea
10	chr1:153479800-153483200	Weak transcription	Placenta	Placenta
11	chr1:153479800-153483200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr1:153479800-153483400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:153479800-153488000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:153480000-153482800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:153480200-153482400	Weak transcription	Stomach Smooth Muscle	stomach
16	chr1:153480200-153483200	Weak transcription	Duodenum Mucosa	Duodenum
17	chr1:153480200-153483400	Weak transcription	Hela-S3	cervix
18	chr1:153480200-153483600	Weak transcription	Stomach Mucosa	stomach
19	chr1:153480200-153488000	Weak transcription	Left Ventricle	heart
20	chr1:153480400-153483200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:153480400-153483400	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr1:153480400-153483600	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr1:153480600-153482000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:153480600-153483400	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr1:153480600-153485400	Weak transcription	Adipose Nuclei	Adipose
26	chr1:153480600-153485400	Weak transcription	Esophagus	oesophagus
27	chr1:153480600-153485400	Weak transcription	Right Atrium	heart
28	chr1:153480800-153483200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr1:153480800-153483400	Weak transcription	Colonic Mucosa	Colon
30	chr1:153480800-153483400	Weak transcription	Fetal Stomach	stomach
31	chr1:153480800-153483400	Weak transcription	NHDF-Ad	bronchial
32	chr1:153480800-153483600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr1:153480800-153487800	Weak transcription	Fetal Intestine Large	intestine
34	chr1:153481000-153481800	Weak transcription	NHLF	lung
35	chr1:153481000-153482200	Weak transcription	Colon Smooth Muscle	Colon
36	chr1:153481000-153483400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:153481000-153483400	Weak transcription	Fetal Muscle Leg	muscle
38	chr1:153481000-153488000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:153481000-153488000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr1:153481000-153488000	Weak transcription	Fetal Intestine Small	intestine
41	chr1:153481000-153490600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr1:153481200-153483200	Weak transcription	Fetal Muscle Trunk	muscle
43	chr1:153481200-153483400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr1:153481200-153483400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr1:153481200-153483400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr1:153481200-153483400	Weak transcription	Osteobl	bone
47	chr1:153481200-153483600	Weak transcription	Ovary	ovary
48	chr1:153481200-153503600	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr1:153481400-153481800	Weak transcription	A549	lung

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