Variant report

Variant	rs10887746
Chromosome Location	chr10:89482833-89482834
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	chr10:89479070..89480697-chr10:89482031..89483577,2	MCF-7	breast:
2	chr10:89418413..89421099-chr10:89482175..89484816,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198682	Chromatin interaction
ENSG00000196566	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10788564	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10788566	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10887745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10887748	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10887749	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10887750	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10887751	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11202525	0.88[EUR][1000 genomes]
rs11202526	1.00[CEU][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11202527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11202530	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11202536	0.81[YRI][hapmap]
rs11202553	0.81[YRI][hapmap]
rs11202557	0.82[YRI][hapmap]
rs11202571	0.81[YRI][hapmap]
rs11596283	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11813070	0.82[CEU][hapmap]
rs12414218	0.82[CEU][hapmap]
rs12414519	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12773536	0.81[YRI][hapmap]
rs1853168	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2302406	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2302407	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34783121	0.86[EUR][1000 genomes]
rs3781187	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3781188	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3781189	0.82[CEU][hapmap]
rs3781190	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3815417	1.00[CEU][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4933459	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4933460	0.82[CEU][hapmap]
rs4933461	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4934363	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];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4934364	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4934365	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4934366	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];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4934367	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];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6586101	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6586102	0.82[YRI][hapmap]
rs7068030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7073722	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7073724	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7079187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7080206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7080768	0.82[CEU][hapmap]
rs7081055	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7088594	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7097745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7896505	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7898500	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7907791	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7908313	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7919607	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7920554	1.00[CEU][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7921017	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10887746	PAPSS2	cis	Muscle Skeletal	GTEx

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:89460400-89512000	Weak transcription	HSMM	muscle
2	chr10:89462200-89494800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr10:89463000-89489400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr10:89463000-89494600	Weak transcription	Fetal Muscle Leg	muscle
5	chr10:89463000-89541400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr10:89466200-89494600	Weak transcription	A549	lung
7	chr10:89466800-89494600	Weak transcription	Hela-S3	cervix
8	chr10:89468600-89494000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr10:89468800-89483200	Strong transcription	Osteobl	bone
10	chr10:89470200-89487000	Weak transcription	Aorta	Aorta
11	chr10:89470600-89493800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr10:89472400-89503000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr10:89473000-89577200	Weak transcription	Gastric	stomach
14	chr10:89473600-89494000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr10:89473800-89493600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr10:89475200-89485600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr10:89475400-89487000	Weak transcription	Placenta	Placenta
18	chr10:89476000-89483000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr10:89476000-89487000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr10:89476000-89494600	Weak transcription	NHDF-Ad	bronchial
21	chr10:89476200-89489800	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr10:89476200-89489800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr10:89476200-89494000	Weak transcription	Fetal Stomach	stomach
24	chr10:89476200-89494600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr10:89476200-89542400	Weak transcription	Pancreas	Pancrea
26	chr10:89476400-89494000	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr10:89476400-89494800	Weak transcription	Spleen	Spleen
28	chr10:89476400-89504800	Weak transcription	Left Ventricle	heart
29	chr10:89477000-89489800	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr10:89477200-89494800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr10:89477400-89500000	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr10:89478000-89494800	Weak transcription	Ovary	ovary
33	chr10:89479200-89485000	Weak transcription	Adipose Nuclei	Adipose
34	chr10:89480000-89484000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr10:89480600-89483000	Enhancers	HUVEC	blood vessel
36	chr10:89480800-89484600	Weak transcription	Lung	lung
37	chr10:89481800-89483400	Strong transcription	NH-A	brain
38	chr10:89481800-89485000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr10:89482000-89483200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
40	chr10:89482200-89483400	Enhancers	Fetal Lung	lung
41	chr10:89482400-89483000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr10:89482400-89483800	Enhancers	Fetal Intestine Small	intestine
43	chr10:89482400-89483800	Enhancers	Fetal Kidney	kidney
44	chr10:89482600-89483400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr10:89482600-89483600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr10:89482600-89483600	Enhancers	Small Intestine	intestine
47	chr10:89482600-89484000	Enhancers	Fetal Intestine Large	intestine
48	chr10:89482800-89483000	Enhancers	Duodenum Mucosa	Duodenum
49	chr10:89482800-89483000	Weak transcription	NHLF	lung
50	chr10:89482800-89483200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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