Variant report

Variant	rs6860568
Chromosome Location	chr5:79258320-79258321
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:79257889..79260201-chr5:79261651..79263210,2	K562	blood:
2	chr5:79253337..79255880-chr5:79257487..79259390,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10035728	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10041212	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10041404	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10043116	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10060444	0.81[CHB][hapmap];0.80[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10062607	0.81[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs10064975	0.81[TSI][hapmap]
rs10065778	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10066471	0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs10071601	0.84[EUR][1000 genomes]
rs10077238	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1017996	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1017997	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1017998	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1032341	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1032342	0.88[ASW][hapmap];0.92[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11741143	0.81[CHB][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs11748289	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13354864	0.86[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1370987	0.81[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs1438739	0.81[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs16877389	1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs2291524	0.82[ASW][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2404708	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2451929	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2451930	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2471104	0.82[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2471105	0.88[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2471106	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2471107	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2471108	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2471109	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs405878	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs422690	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6453494	0.83[EUR][1000 genomes]
rs6453495	0.81[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs6453496	0.81[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs6453497	1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs6865678	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6868916	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6870377	0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6873684	0.84[EUR][1000 genomes]
rs6882768	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6887873	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6892826	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7446065	0.86[CHB][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7734858	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs923634	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs923636	0.94[ASW][hapmap];0.92[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9293795	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs963423	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs963424	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][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	esv1822393	chr5:79195538-79260489	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6860568	THBS4	cis	lymphoblastoid	seeQTL
rs6860568	MTX3	Cis_1M	lymphoblastoid	RTeQTL
rs6860568	THBS4	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79257200-79258800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:79257400-79258800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:79257400-79259000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr5:79257400-79260000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr5:79257600-79258800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr5:79257600-79259000	Enhancers	NHEK	skin
7	chr5:79257600-79259400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr5:79257800-79259000	Enhancers	HMEC	breast
9	chr5:79257800-79259200	Enhancers	Fetal Muscle Leg	muscle
10	chr5:79257800-79259400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:79257800-79259400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:79257800-79259400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr5:79257800-79260000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr5:79258000-79259000	Enhancers	Fetal Brain Male	brain
15	chr5:79258000-79259000	Enhancers	NH-A	brain
16	chr5:79258200-79258400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr5:79258200-79258600	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr5:79258200-79258800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr5:79258200-79258800	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr5:79258200-79258800	Enhancers	Primary hematopoietic stem cells	blood
21	chr5:79258200-79259000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
22	chr5:79258200-79259000	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr5:79258200-79259000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr5:79258200-79259000	Enhancers	HSMM	muscle
25	chr5:79258200-79259200	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr5:79258200-79259200	Enhancers	NHLF	lung
27	chr5:79258200-79259600	Enhancers	NHDF-Ad	bronchial

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