Variant report

Variant	rs7752414
Chromosome Location	chr6:87915822-87915823
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:87910678..87912496-chr6:87913954..87916922,2	MCF-7	breast:
2	chr6:87862757..87864268-chr6:87915198..87917415,2	MCF-7	breast:
3	chr6:87914519..87917049-chr6:87918651..87921686,3	MCF-7	breast:

Extended variants
information (count: 117 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs1145712	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap]
rs1145713	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1145714	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[EUR][1000 genomes]
rs1145715	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes]
rs1145716	0.82[EUR][1000 genomes]
rs11759727	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1188806	0.82[EUR][1000 genomes]
rs1188816	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1188817	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap]
rs1188819	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs1203162	0.92[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes]
rs1203163	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1203164	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[EUR][1000 genomes]
rs12211627	0.80[ASW][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap]
rs13201289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13210074	0.84[EUR][1000 genomes]
rs16878497	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1739886	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1746444	1.00[ASW][hapmap];0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap]
rs1753152	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs1925686	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1925689	0.81[CEU][hapmap]
rs2025490	0.85[EUR][1000 genomes]
rs2147917	0.81[CEU][hapmap]
rs2147918	0.81[CEU][hapmap]
rs2236048	0.81[EUR][1000 genomes]
rs242263	0.91[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs242264	0.80[ASW][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs242265	0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs242268	0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs242269	0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs242275	1.00[ASW][hapmap];0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap]
rs242276	1.00[ASW][hapmap];0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap]
rs242282	0.80[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.81[EUR][1000 genomes]
rs2983136	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.81[EUR][1000 genomes]
rs368267	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3734187	0.81[CEU][hapmap]
rs374792	1.00[ASW][hapmap];0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap]
rs377288	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs379455	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs3812130	0.81[CEU][hapmap]
rs381798	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap]
rs382956	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs384318	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3846776	0.81[CEU][hapmap]
rs3857483	0.84[CEU][hapmap]
rs3857484	0.81[CEU][hapmap]
rs3857486	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs397516	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs398140	0.98[CHD][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap]
rs3999791	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs406981	0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs4099964	0.81[CEU][hapmap]
rs410683	0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs411606	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs413687	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs414453	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4235830	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs440296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs452315	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs4707344	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4707345	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4707348	0.81[CEU][hapmap]
rs4707355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs540975	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs541170	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs6907805	0.81[CEU][hapmap]
rs6908834	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6913159	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6913932	0.81[CEU][hapmap]
rs6921007	0.81[CEU][hapmap]
rs6921673	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6926686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6927748	0.82[CEU][hapmap]
rs6932641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6933046	0.81[CEU][hapmap]
rs6934603	0.81[CEU][hapmap]
rs6938885	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6939075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6940325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6940544	0.80[CEU][hapmap]
rs7755883	0.81[CEU][hapmap]
rs7757330	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7758360	0.94[ASN][1000 genomes]
rs7767245	0.83[EUR][1000 genomes]
rs7774603	0.81[CEU][hapmap]
rs910564	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs912815	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9294375	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9294376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9344691	0.85[CEU][hapmap]
rs9344695	0.81[CEU][hapmap]
rs9353468	0.81[CEU][hapmap]
rs9359743	0.81[CEU][hapmap]
rs9362411	0.81[CEU][hapmap]
rs9362415	0.81[CEU][hapmap]
rs9444476	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9444481	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9444486	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9444488	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9444490	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9444491	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9450619	0.85[EUR][1000 genomes]
rs9450623	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9450630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9450636	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9450637	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9450638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9450639	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9450640	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9450646	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9450650	0.81[CEU][hapmap]
rs9450651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9450652	0.81[CEU][hapmap]
rs9450653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[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	esv2758067	chr6:87817883-87992957	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2759453	chr6:87817883-87992957	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic 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	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs7752414	ZNF292	cis	Lymphoblastoid	GTEx
rs7752414	C6orf162	cis	parietal	SCAN
rs7752414	SLC35A1	cis	parietal	SCAN
rs7752414	C6orf162	cis	multi-tissue	Pritchard
rs7752414	C6orf162	cis	cerebellum	SCAN
rs7752414	MDN1	cis	parietal	SCAN
rs7752414	C6orf162	Cis_1M	lymphoblastoid	RTeQTL
rs7752414	Hs.485895	cis	multi-tissue	Pritchard
rs7752414	C6orf163	Cis_1M	lymphoblastoid	RTeQTL
rs7752414	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs7752414	C6orf163	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:87868000-87933000	Weak transcription	Hela-S3	cervix
2	chr6:87874400-87924200	Weak transcription	Fetal Kidney	kidney
3	chr6:87879800-87923000	Weak transcription	Esophagus	oesophagus
4	chr6:87881400-87926200	Weak transcription	Liver	Liver
5	chr6:87883400-87926200	Weak transcription	Fetal Lung	lung
6	chr6:87884000-87964400	Weak transcription	NHEK	skin
7	chr6:87888200-87964200	Weak transcription	HSMMtube	muscle
8	chr6:87889800-87926400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:87890800-87933000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:87891000-87920000	Weak transcription	Placenta	Placenta
11	chr6:87891000-87956000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:87891200-87929200	Weak transcription	Thymus	Thymus
13	chr6:87891400-87932600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr6:87892000-87923000	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr6:87892800-87921600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr6:87893000-87917600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr6:87894800-87921800	Weak transcription	NHDF-Ad	bronchial
18	chr6:87894800-87924200	Weak transcription	Adipose Nuclei	Adipose
19	chr6:87894800-87926200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:87895800-87924000	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr6:87896000-87932800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr6:87896200-87920200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr6:87896200-87921400	Weak transcription	HepG2	liver
24	chr6:87896400-87925600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr6:87896400-87926000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr6:87896400-87927400	Weak transcription	HMEC	breast
27	chr6:87896400-87927800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr6:87896600-87923200	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr6:87896600-87925600	Weak transcription	HSMM	muscle
30	chr6:87905200-87950200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr6:87906200-87921800	Weak transcription	Brain Hippocampus Middle	brain
32	chr6:87906200-87956200	Weak transcription	A549	lung
33	chr6:87906400-87917600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr6:87906400-87919200	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr6:87906400-87920200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr6:87906400-87964400	Weak transcription	NHLF	lung
37	chr6:87907400-87930800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr6:87907800-87929200	Weak transcription	Fetal Muscle Trunk	muscle
39	chr6:87908800-87918800	Weak transcription	Rectal Smooth Muscle	rectum
40	chr6:87909000-87928400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr6:87909000-87929800	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr6:87909800-87918600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr6:87909800-87918600	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr6:87909800-87918600	Weak transcription	Small Intestine	intestine
45	chr6:87909800-87921600	Weak transcription	Gastric	stomach
46	chr6:87910200-87934400	Weak transcription	Fetal Brain Male	brain
47	chr6:87910400-87921800	Weak transcription	Brain Substantia Nigra	brain
48	chr6:87910400-87922000	Weak transcription	Brain Angular Gyrus	brain
49	chr6:87910400-87922400	Weak transcription	Brain Germinal Matrix	brain
50	chr6:87910400-87922600	Weak transcription	Skeletal Muscle Female	skeletal muscle

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