Variant report

Variant	rs7446065
Chromosome Location	chr5:79273042-79273043
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	chr5:79262485..79266204-chr5:79269459..79273570,3	MCF-7	breast:
2	chr5:79271074..79273933-chr5:79292218..79294924,2	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10035728	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10041212	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10041404	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10043116	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10060444	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10062607	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10064975	0.95[CEU][hapmap];0.91[GIH][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap]
rs10065778	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10066471	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10071601	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10077238	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1017996	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1017997	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1017998	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1032341	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1032342	0.88[ASW][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap];0.80[AMR][1000 genomes]
rs11741143	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11748289	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13354864	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1370987	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1438739	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16877389	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2059794	0.81[YRI][hapmap]
rs2291524	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.84[LWK][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2404708	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2451929	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2451930	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2471104	0.95[JPT][hapmap];0.80[YRI][hapmap]
rs2471105	0.82[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2471107	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2471108	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2471109	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs405878	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs422690	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6453494	0.93[EUR][1000 genomes]
rs6453495	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6453496	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6453497	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6860568	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6865678	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6868916	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6870377	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6873684	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6882768	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6887873	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6892826	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7734858	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs923634	0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs923636	0.83[ASW][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9293795	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs963423	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs963424	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021113	chr5:79034662-79289828	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7446065	THBS4	cis	lymphoblastoid	seeQTL
rs7446065	MTX3	Cis_1M	lymphoblastoid	RTeQTL
rs7446065	THBS4	cis	cerebellum	SCAN
rs7446065	ACOT12	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79260600-79286200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:79263200-79273200	Weak transcription	Psoas Muscle	Psoas
3	chr5:79267800-79273600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr5:79268000-79273800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr5:79268400-79273600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr5:79269000-79286400	Weak transcription	Thymus	Thymus
7	chr5:79269200-79274800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr5:79269400-79277800	Weak transcription	Hela-S3	cervix
9	chr5:79269400-79279200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr5:79269600-79273200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr5:79269600-79273200	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr5:79269600-79273800	Weak transcription	Colonic Mucosa	Colon
13	chr5:79269600-79276000	Weak transcription	Brain Hippocampus Middle	brain
14	chr5:79269600-79276600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr5:79269600-79277800	Weak transcription	Brain Anterior Caudate	brain
16	chr5:79269800-79273600	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr5:79269800-79273600	Weak transcription	Brain Germinal Matrix	brain
18	chr5:79269800-79279200	Weak transcription	Brain Substantia Nigra	brain
19	chr5:79269800-79279400	Weak transcription	Lung	lung
20	chr5:79269800-79281400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr5:79269800-79286000	Weak transcription	Fetal Heart	heart
22	chr5:79270000-79273800	Weak transcription	Esophagus	oesophagus
23	chr5:79270000-79276400	Strong transcription	Primary B cells from cord blood	blood
24	chr5:79270000-79276400	Weak transcription	Fetal Kidney	kidney
25	chr5:79270000-79286000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr5:79270200-79276000	Weak transcription	Colon Smooth Muscle	Colon
27	chr5:79270200-79286400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr5:79270400-79273200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr5:79270400-79273600	Weak transcription	Ovary	ovary
30	chr5:79270400-79276400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr5:79270600-79278400	Weak transcription	HepG2	liver
32	chr5:79270800-79273200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr5:79270800-79275400	Strong transcription	Primary T cells from cord blood	blood
34	chr5:79270800-79276200	Strong transcription	Liver	Liver
35	chr5:79270800-79284800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr5:79271000-79273400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr5:79271000-79273800	Weak transcription	Fetal Intestine Small	intestine
38	chr5:79271000-79275200	Strong transcription	Primary hematopoietic stem cells	blood
39	chr5:79271000-79286400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr5:79271200-79273200	Weak transcription	Osteobl	bone
41	chr5:79271200-79279400	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr5:79271200-79280400	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr5:79271200-79281000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr5:79271200-79282000	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr5:79271200-79285200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr5:79271200-79285800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr5:79271200-79285800	Weak transcription	NHLF	lung
48	chr5:79271400-79277800	Weak transcription	NH-A	brain
49	chr5:79271400-79284000	Weak transcription	HSMMtube	muscle
50	chr5:79271400-79285400	Strong transcription	HUES64 Cell Line	embryonic stem cell

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