Variant report

Variant	rs7746465
Chromosome Location	chr6:88348996-88348997
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:88348849..88351685-chr6:88355176..88357576,2	MCF-7	breast:

Extended variants
information (count: 99 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs1051131	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.82[EUR][1000 genomes]
rs1051148	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.85[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.81[EUR][1000 genomes]
rs10755484	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13193380	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13194003	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13214153	0.86[CHB][hapmap]
rs2207144	0.86[CHB][hapmap];0.84[GIH][hapmap]
rs2207146	0.96[CEU][hapmap];0.91[CHB][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.96[TSI][hapmap]
rs2246113	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2268993	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap]
rs2268994	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs2273129	0.96[CEU][hapmap];0.91[CHB][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap]
rs2284908	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs2300906	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs2300909	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs2307379	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2325064	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2754245	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap]
rs2754247	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2754248	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2754260	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2754262	1.00[CEU][hapmap];0.80[CHD][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2787893	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2787921	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2787924	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2787927	1.00[CEU][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap]
rs2814712	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3757368	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3918467	0.96[CEU][hapmap];0.91[CHB][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap]
rs3934838	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4334949	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4464759	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4498321	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4587138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4587143	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4706294	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4707373	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4707374	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4707376	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4707377	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4707379	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4707382	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4707383	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6454631	0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6454632	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6454636	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6454638	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6454640	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6454641	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6905947	0.86[CHB][hapmap]
rs6906769	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6908386	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6914299	0.86[CHB][hapmap]
rs6916732	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6918909	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6923230	0.81[EUR][1000 genomes]
rs6928160	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6930600	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6931069	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6933587	0.86[CHB][hapmap]
rs6940150	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7741825	0.86[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7742965	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7750207	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7752494	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7755167	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7757636	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7757794	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7761814	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs7762864	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7772561	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7773906	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9294379	0.86[CHB][hapmap]
rs9294381	0.86[CHB][hapmap]
rs9444504	0.96[CEU][hapmap];0.91[CHB][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap]
rs9444512	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9444519	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9444522	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9444524	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9444525	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9444526	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9444530	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450701	0.86[CHB][hapmap];0.84[GIH][hapmap];0.81[MEX][hapmap]
rs9450704	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs9450712	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs9450723	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.80[YRI][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9450732	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9450733	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9450738	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9450739	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9450744	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9450752	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9450755	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9450762	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs985764	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]

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	nsv1031961	chr6:88110401-88367006	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1031460	chr6:88153079-88410050	Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv1026482	chr6:88164934-88409728	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1027706	chr6:88168987-88409728	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs7746465	SNORD50A	cis	cerebellum	SCAN
rs7746465	C6orf162	cis	parietal	SCAN
rs7746465	C6orf166	Cis_1M	lymphoblastoid	RTeQTL
rs7746465	SLC35A1	cis	multi-tissue	Pritchard
rs7746465	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs7746465	SLC35A1	cis	parietal	SCAN
rs7746465	ZNF567	trans	lymphoblastoid	RTeQTL
rs7746465	SLC35A1	cis	lymphoblastoid	seeQTL
rs7746465	C6orf162	cis	cerebellum	SCAN
rs7746465	C6orf162	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88300600-88391200	Weak transcription	Colonic Mucosa	Colon
2	chr6:88301200-88385000	Weak transcription	Colon Smooth Muscle	Colon
3	chr6:88301400-88354400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr6:88301400-88354600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr6:88302000-88354400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr6:88302000-88354600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr6:88305000-88398800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr6:88308800-88369800	Weak transcription	Fetal Brain Male	brain
9	chr6:88312200-88371200	Weak transcription	NHEK	skin
10	chr6:88312400-88380600	Weak transcription	Brain Substantia Nigra	brain
11	chr6:88314000-88384800	Weak transcription	Hela-S3	cervix
12	chr6:88314200-88399200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr6:88314600-88385000	Weak transcription	Esophagus	oesophagus
14	chr6:88316600-88381200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:88316600-88390000	Weak transcription	Pancreas	Pancrea
16	chr6:88320400-88400800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr6:88321600-88350000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr6:88322000-88352800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr6:88322800-88382000	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr6:88323000-88366400	Weak transcription	A549	lung
21	chr6:88324000-88369800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr6:88324000-88385000	Weak transcription	Gastric	stomach
23	chr6:88324200-88350600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr6:88324200-88366600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr6:88324200-88369000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr6:88324200-88370200	Weak transcription	Psoas Muscle	Psoas
27	chr6:88324200-88378200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr6:88324200-88380400	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr6:88325400-88369200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr6:88327200-88362000	Weak transcription	Fetal Heart	heart
31	chr6:88328400-88357000	Weak transcription	HUVEC	blood vessel
32	chr6:88329800-88383200	Weak transcription	Lung	lung
33	chr6:88332200-88350200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr6:88333400-88354600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr6:88333400-88384800	Weak transcription	Brain Angular Gyrus	brain
36	chr6:88334600-88362600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr6:88337800-88351800	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr6:88337800-88352000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr6:88338800-88369600	Weak transcription	HSMMtube	muscle
40	chr6:88339000-88354400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr6:88339200-88396800	Weak transcription	Right Ventricle	heart
42	chr6:88340000-88354200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr6:88340000-88370000	Weak transcription	Spleen	Spleen
44	chr6:88340200-88349000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr6:88340200-88364400	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr6:88340600-88364400	Weak transcription	NHLF	lung
47	chr6:88340600-88368400	Weak transcription	NHDF-Ad	bronchial
48	chr6:88341600-88349000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr6:88341800-88350200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr6:88342000-88349000	Weak transcription	Fetal Intestine Small	intestine

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