Variant report

Variant	rs10060444
Chromosome Location	chr5:79274595-79274596
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10035728	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10041212	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10041404	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10043116	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10062607	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10064975	0.95[CEU][hapmap];0.89[GIH][hapmap];0.88[TSI][hapmap]
rs10065778	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10066471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10071601	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10077238	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1017996	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1017997	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1017998	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1032341	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1032342	0.80[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs11741143	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11748289	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13354864	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1370987	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1438739	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16877389	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2291524	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2404708	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2451929	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2451930	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2471104	1.00[JPT][hapmap]
rs2471105	0.80[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2471107	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2471108	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2471109	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs405878	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs422690	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6453494	0.92[EUR][1000 genomes]
rs6453495	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6453496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6453497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6860568	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6865678	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6868916	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6870377	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6873684	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6882768	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6887873	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6892826	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7446065	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]
rs7707036	0.84[ASN][1000 genomes]
rs7734858	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs923634	0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs923636	0.80[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9293795	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs963423	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs963424	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	esv2763465	chr5:79274595-79278596	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10060444	THBS4	cis	cerebellum	SCAN
rs10060444	ACOT12	cis	cerebellum	SCAN
rs10060444	MTX3	Cis_1M	lymphoblastoid	RTeQTL
rs10060444	THBS4	cis	lymphoblastoid	seeQTL

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	chr5:79269000-79286400	Weak transcription	Thymus	Thymus
3	chr5:79269200-79274800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr5:79269400-79277800	Weak transcription	Hela-S3	cervix
5	chr5:79269400-79279200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr5:79269600-79276000	Weak transcription	Brain Hippocampus Middle	brain
7	chr5:79269600-79276600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr5:79269600-79277800	Weak transcription	Brain Anterior Caudate	brain
9	chr5:79269800-79279200	Weak transcription	Brain Substantia Nigra	brain
10	chr5:79269800-79279400	Weak transcription	Lung	lung
11	chr5:79269800-79281400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr5:79269800-79286000	Weak transcription	Fetal Heart	heart
13	chr5:79270000-79276400	Strong transcription	Primary B cells from cord blood	blood
14	chr5:79270000-79276400	Weak transcription	Fetal Kidney	kidney
15	chr5:79270000-79286000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr5:79270200-79276000	Weak transcription	Colon Smooth Muscle	Colon
17	chr5:79270200-79286400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:79270400-79276400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr5:79270600-79278400	Weak transcription	HepG2	liver
20	chr5:79270800-79275400	Strong transcription	Primary T cells from cord blood	blood
21	chr5:79270800-79276200	Strong transcription	Liver	Liver
22	chr5:79270800-79284800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr5:79271000-79275200	Strong transcription	Primary hematopoietic stem cells	blood
24	chr5:79271000-79286400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr5:79271200-79279400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr5:79271200-79280400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr5:79271200-79281000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr5:79271200-79282000	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr5:79271200-79285200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr5:79271200-79285800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr5:79271200-79285800	Weak transcription	NHLF	lung
32	chr5:79271400-79277800	Weak transcription	NH-A	brain
33	chr5:79271400-79284000	Weak transcription	HSMMtube	muscle
34	chr5:79271400-79285400	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr5:79271400-79286000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr5:79271400-79286000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr5:79271600-79277800	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr5:79271600-79280800	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr5:79271600-79286000	Weak transcription	HUVEC	blood vessel
40	chr5:79271800-79277800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr5:79272200-79279400	Weak transcription	Spleen	Spleen
42	chr5:79272200-79286400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr5:79272400-79277000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr5:79272400-79279400	Weak transcription	Right Ventricle	heart
45	chr5:79272400-79285000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr5:79272400-79286400	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr5:79272400-79286400	Weak transcription	Pancreas	Pancrea
48	chr5:79272600-79275200	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr5:79272600-79284800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr5:79272600-79285000	Strong transcription	HUES48 Cell Line	embryonic stem cell

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