Variant report

Variant	rs2471105
Chromosome Location	chr5:79252182-79252183
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:79243051..79245888-chr5:79249775..79252734,2	K562	blood:
2	chr5:79233060..79235575-chr5:79249554..79252283,4	MCF-7	breast:
3	chr5:79249486..79252419-chr5:79253972..79256405,2	MCF-7	breast:
4	chr5:79250469..79253672-chr5:79285038..79288543,6	MCF-7	breast:
5	chr5:79251016..79252738-chr5:79254951..79256533,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113296	Chromatin interaction
ENSG00000177034	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10035728	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10041212	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10041404	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10043116	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10060444	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]
rs10062607	0.95[JPT][hapmap];0.80[EUR][1000 genomes]
rs10064975	0.81[TSI][hapmap]
rs10065778	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10066471	0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs10071601	0.81[EUR][1000 genomes]
rs10077238	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1017996	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1017997	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1017998	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1032341	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1032342	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11741143	0.82[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs11748289	0.80[AMR][1000 genomes]
rs13354864	0.82[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.84[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1370987	0.82[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.80[EUR][1000 genomes]
rs1438739	0.82[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs16877389	0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs2291524	0.82[ASW][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2404708	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2451929	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2451930	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2471104	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2471106	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2471107	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2471108	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2471109	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs405878	0.80[EUR][1000 genomes]
rs422690	0.80[EUR][1000 genomes]
rs6453495	0.82[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs6453496	0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs6453497	0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs6860568	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6865678	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6868916	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6870377	0.95[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs6873684	0.80[EUR][1000 genomes]
rs6882768	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6887873	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6892826	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7446065	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]
rs7734858	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs923634	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];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs923636	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9293795	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs963423	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs963424	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2471105	THBS4	cis	cerebellum	SCAN
rs2471105	THBS4	cis	lymphoblastoid	seeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79250400-79252600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr5:79250400-79252600	Enhancers	NHDF-Ad	bronchial
3	chr5:79250600-79252600	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr5:79250600-79252600	Enhancers	Fetal Muscle Leg	muscle
5	chr5:79250800-79252400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr5:79250800-79252600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr5:79250800-79252600	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr5:79250800-79252600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr5:79250800-79252600	Enhancers	HMEC	breast
10	chr5:79250800-79252800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr5:79250800-79253400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:79250800-79253600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:79251000-79252400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr5:79251000-79252400	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr5:79251000-79254000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr5:79251200-79252200	Weak transcription	Esophagus	oesophagus
17	chr5:79251200-79252600	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr5:79251200-79252600	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr5:79251200-79252800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr5:79251200-79252800	Enhancers	HSMM	muscle
21	chr5:79251600-79252200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
22	chr5:79251600-79252400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr5:79251600-79252400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr5:79251600-79252600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr5:79251600-79252800	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr5:79251600-79252800	Enhancers	Muscle Satellite Cultured Cells	--
27	chr5:79251600-79253200	Enhancers	HSMMtube	muscle
28	chr5:79251600-79253400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr5:79251800-79252600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr5:79251800-79252800	Enhancers	NH-A	brain
31	chr5:79251800-79257600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr5:79252000-79252400	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr5:79252000-79252600	Enhancers	NHLF	lung
34	chr5:79252000-79252800	Flanking Active TSS	NHEK	skin
35	chr5:79252000-79252800	Enhancers	Osteobl	bone

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