Variant report

Variant	rs7745603
Chromosome Location	chr6:27090404-27090405
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:196013815..196016163-chr6:27090213..27092532,2	MCF-7	breast:
2	chr6:26027124..26029972-chr6:27089042..27090652,2	K562	blood:
3	chr6:27089344..27092016-chr6:27112372..27115095,4	MCF-7	breast:
4	chr6:26594405..26597151-chr6:27087903..27090496,2	K562	blood:

Variant related genes	Relation type
ENSG00000161217	Chromatin interaction
ENSG00000124529	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000197903	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1028308	0.80[TSI][hapmap]
rs2393918	0.89[JPT][hapmap]
rs4358615	0.89[JPT][hapmap]
rs4582379	0.89[JPT][hapmap]
rs6456769	0.89[JPT][hapmap]
rs6916301	0.93[ASN][1000 genomes]
rs6921388	0.80[JPT][hapmap];0.80[TSI][hapmap]
rs6922098	0.82[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6933999	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73401108	0.90[ASN][1000 genomes]
rs73401117	0.90[ASN][1000 genomes]
rs7744759	0.80[TSI][hapmap]
rs7745588	0.84[ASN][1000 genomes]
rs7761889	0.90[ASN][1000 genomes]
rs911186	0.82[CEU][hapmap];0.80[TSI][hapmap]
rs9295730	0.80[TSI][hapmap]
rs9348743	0.82[CHB][hapmap]
rs9357031	0.93[ASN][1000 genomes]
rs9368489	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9379960	0.80[TSI][hapmap]
rs9379961	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9379962	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9393790	0.88[ASW][hapmap];0.84[GIH][hapmap];0.81[LWK][hapmap];0.80[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs9393791	0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs9467989	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs994690	0.82[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	esv2758038	chr6:26695219-27095714	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
3	esv2759410	chr6:26695219-27095714	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
4	nsv1029124	chr6:26825468-27109774	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	244 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs7745603	BTN3A3	cis	lymphoblastoid	seeQTL
rs7745603	BTN3A2	cis	lymphoblastoid	seeQTL
rs7745603	HIST1H2BF	cis	parietal	SCAN
rs7745603	BTN3A2	cis	multi-tissue	Pritchard
rs7745603	BTN3A2///BTN3A3	Cis_1M	lymphoblastoid	RTeQTL
rs7745603	ZKSCAN3	cis	parietal	SCAN
rs7745603	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL
rs7745603	BTN2A1	Cis_1M	lymphoblastoid	RTeQTL
rs7745603	HIST1H2BH	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27080800-27094400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr6:27081200-27094600	Weak transcription	Psoas Muscle	Psoas
3	chr6:27083000-27094400	Weak transcription	Hela-S3	cervix
4	chr6:27085800-27094400	Weak transcription	Fetal Heart	heart
5	chr6:27086200-27094400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:27086200-27094400	Weak transcription	Left Ventricle	heart
7	chr6:27086400-27099200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:27087000-27094400	Weak transcription	A549	lung
9	chr6:27087200-27094000	Weak transcription	Fetal Thymus	thymus
10	chr6:27087600-27094400	Weak transcription	Fetal Lung	lung
11	chr6:27087800-27094400	Weak transcription	Primary B cells from cord blood	blood
12	chr6:27088200-27094400	Weak transcription	Thymus	Thymus
13	chr6:27088800-27094200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr6:27088800-27094400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr6:27089000-27094400	Weak transcription	Primary T cells from cord blood	blood
16	chr6:27089000-27094600	Weak transcription	Fetal Intestine Small	intestine
17	chr6:27089200-27092000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr6:27089200-27093800	Weak transcription	Dnd41	blood
19	chr6:27089200-27094000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr6:27089200-27094000	Weak transcription	GM12878-XiMat	blood
21	chr6:27089200-27094400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr6:27089200-27094400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr6:27089200-27094600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr6:27089200-27094600	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr6:27089200-27094600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr6:27089200-27094600	Weak transcription	NHEK	skin
27	chr6:27089400-27094000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr6:27089400-27094000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr6:27089400-27094600	Weak transcription	Fetal Intestine Large	intestine
30	chr6:27090200-27090800	Genic enhancers	K562	blood
31	chr6:27090400-27091000	Strong transcription	Placenta	Placenta
32	chr6:27090400-27094400	Weak transcription	HSMMtube	muscle

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