Variant report

Variant	rs7758703
Chromosome Location	chr6:133085417-133085418
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ESR1	chr6:133085202-133085592	T-47D	breast:	n/a	chr6:133085423-133085440 chr6:133085422-133085439
2	FOS	chr6:133085263-133085892	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr6:133085244-133085884	MCF10A-Er-Src	breast:	n/a	n/a
4	ESR1	chr6:133085212-133085536	T-47D	breast:	n/a	chr6:133085423-133085440 chr6:133085422-133085439

No.	Distal block	Cell Line	Cell type
1	chr6:133084415..133087080-chr6:133134762..133137402,2	MCF-7	breast:
2	chr6:133054047..133059196-chr6:133082600..133087082,5	MCF-7	breast:
3	chr6:133084618..133086907-chr6:133118822..133121566,2	K562	blood:
4	chr6:133084942..133087324-chr6:133134860..133137280,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271488	TF binding region
VNN2	TF binding region
ENSG00000093134	Chromatin interaction
ENSG00000206754	Chromatin interaction
ENSG00000112306	Chromatin interaction
ENSG00000146409	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10457591	1.00[CHB][hapmap]
rs10457596	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10484629	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1122175	0.82[YRI][hapmap]
rs1128998	1.00[CHB][hapmap]
rs11962883	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11964512	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12190684	1.00[CHB][hapmap]
rs12197430	1.00[CHB][hapmap]
rs12198849	0.83[ASN][1000 genomes]
rs12203977	1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12204027	1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12211701	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1467403	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1467404	0.94[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813347	1.00[CHB][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58832890	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61421874	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62424539	0.83[ASN][1000 genomes]
rs6569847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6569848	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6910639	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6912936	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6915168	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6934161	0.83[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73554431	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7738071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7738400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7761365	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7765224	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7769051	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7770081	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9321367	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9321371	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9375919	1.00[CHB][hapmap]
rs9389032	1.00[CHB][hapmap]
rs9399041	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9402452	1.00[CHB][hapmap]
rs9402453	1.00[CHB][hapmap]
rs9402455	1.00[CHB][hapmap]
rs9493435	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9493436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9493437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9493438	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9493443	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9493444	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9493445	1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9493446	0.83[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9493454	0.88[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes];0.86[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	nsv532069	chr6:132776411-133462292	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv1015742	chr6:132933666-133285852	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7758703	C6orf192	cis	multi-tissue	Pritchard
rs7758703	C6orf192	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:133061400-133098000	Weak transcription	Spleen	Spleen
2	chr6:133065000-133098000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:133081400-133096800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:133081800-133086800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr6:133083200-133085800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
6	chr6:133083200-133086000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr6:133083200-133086600	Enhancers	Fetal Intestine Large	intestine
8	chr6:133083400-133090600	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr6:133083600-133099000	Weak transcription	Left Ventricle	heart
10	chr6:133083800-133118200	Weak transcription	Brain Cingulate Gyrus	brain
11	chr6:133084000-133089000	Weak transcription	Fetal Intestine Small	intestine
12	chr6:133084400-133085800	Enhancers	Placenta	Placenta
13	chr6:133084600-133085800	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr6:133084600-133085800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr6:133084600-133085800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr6:133084600-133086000	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr6:133084600-133087000	Enhancers	Fetal Stomach	stomach
18	chr6:133084600-133091200	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr6:133084800-133085600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:133084800-133085600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr6:133084800-133085600	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr6:133084800-133085600	Enhancers	Stomach Mucosa	stomach
23	chr6:133084800-133085800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr6:133084800-133086400	Enhancers	HMEC	breast
25	chr6:133084800-133086400	Enhancers	NHLF	lung
26	chr6:133084800-133089400	Weak transcription	Fetal Thymus	thymus
27	chr6:133084800-133091800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr6:133084800-133097000	Weak transcription	Fetal Muscle Leg	muscle
29	chr6:133085000-133085600	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr6:133085000-133085600	Enhancers	Colon Smooth Muscle	Colon
31	chr6:133085000-133085600	Enhancers	A549	lung
32	chr6:133085000-133085600	Enhancers	Monocytes-CD14+_RO01746	blood
33	chr6:133085000-133085800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr6:133085000-133085800	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr6:133085000-133085800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr6:133085000-133086000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr6:133085000-133086000	Enhancers	Hela-S3	cervix
38	chr6:133085000-133086000	Enhancers	NHEK	skin
39	chr6:133085000-133086400	Enhancers	Adipose Nuclei	Adipose
40	chr6:133085000-133086600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr6:133085000-133086600	Enhancers	NHDF-Ad	bronchial
42	chr6:133085000-133109000	Weak transcription	GM12878-XiMat	blood
43	chr6:133085000-133114600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr6:133085000-133119000	Weak transcription	Thymus	Thymus
45	chr6:133085200-133085800	Enhancers	Aorta	Aorta
46	chr6:133085200-133086000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr6:133085200-133086000	Enhancers	HSMMtube	muscle
48	chr6:133085200-133086000	Enhancers	NH-A	brain
49	chr6:133085200-133086200	Enhancers	Muscle Satellite Cultured Cells	--
50	chr6:133085200-133086200	Enhancers	Osteobl	bone

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