Variant report

Variant	rs17192279
Chromosome Location	chr6:76602995-76602996
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:76600564..76603457-chr6:76615084..76617457,2	MCF-7	breast:
2	chr6:76602974..76603706-chr6:76641806..76642424,2	MCF-7	breast:
3	chr6:76564297..76564995-chr6:76602725..76603462,2	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10498904	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11753849	1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11755704	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11758543	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12664049	0.95[CEU][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1280038	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1280040	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1280050	0.85[CHB][hapmap]
rs1280053	0.85[CHB][hapmap]
rs1280054	0.85[CHB][hapmap]
rs1280058	0.82[CHB][hapmap]
rs17189990	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17191306	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17192223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17794529	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17800625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2104203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2295936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2748957	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2748960	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2748963	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2748966	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs276695	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2842541	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2842543	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2842545	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2842547	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3765140	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3798425	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3798433	0.95[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3798434	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798435	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3818310	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56006932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57920948	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61237402	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62414763	0.83[ASN][1000 genomes]
rs62414769	0.81[ASN][1000 genomes]
rs62414787	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62414789	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62414791	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62414798	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62414800	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62414802	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62414803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62414804	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62414824	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72890660	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7748145	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7761004	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7773977	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9250	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs999209	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019328	chr6:76154751-76604197	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
2	nsv538314	chr6:76154751-76604197	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
3	nsv1021090	chr6:76306100-76759397	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv538318	chr6:76306100-76759397	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv1032961	chr6:76343575-76788852	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv932201	chr6:76365548-77219650	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv1028340	chr6:76410921-76960225	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
8	nsv538319	chr6:76410921-76960225	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17192279	SENP6	Cis_1M	lymphoblastoid	RTeQTL
rs17192279	SENP6	cis	Whole Blood	GTEx

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:76543000-76615000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:76544400-76603800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr6:76566200-76604600	Weak transcription	Right Ventricle	heart
4	chr6:76567000-76604400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr6:76567600-76604200	Weak transcription	NHLF	lung
6	chr6:76573000-76624000	Weak transcription	Placenta	Placenta
7	chr6:76573200-76604200	Weak transcription	Colonic Mucosa	Colon
8	chr6:76573600-76606200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr6:76573800-76607200	Weak transcription	Gastric	stomach
10	chr6:76573800-76608400	Weak transcription	Esophagus	oesophagus
11	chr6:76574400-76632600	Weak transcription	Spleen	Spleen
12	chr6:76576000-76604000	Weak transcription	Fetal Brain Female	brain
13	chr6:76577200-76624600	Weak transcription	Fetal Kidney	kidney
14	chr6:76583400-76606200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr6:76583800-76603000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr6:76583800-76624600	Weak transcription	Pancreas	Pancrea
17	chr6:76584000-76605600	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr6:76584200-76608400	Weak transcription	Aorta	Aorta
19	chr6:76584200-76629400	Weak transcription	Ovary	ovary
20	chr6:76584400-76623800	Weak transcription	Lung	lung
21	chr6:76584800-76615200	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr6:76584800-76644600	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr6:76585000-76608200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr6:76585800-76608000	Weak transcription	NH-A	brain
25	chr6:76585800-76624000	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr6:76585800-76624400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr6:76585800-76626800	Weak transcription	Left Ventricle	heart
28	chr6:76585800-76644600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr6:76586000-76627600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr6:76586200-76624400	Weak transcription	Stomach Smooth Muscle	stomach
31	chr6:76586400-76607800	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr6:76587600-76623800	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr6:76589000-76603200	Weak transcription	Brain Cingulate Gyrus	brain
34	chr6:76591600-76603200	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr6:76592000-76606000	Weak transcription	Adipose Nuclei	Adipose
36	chr6:76592200-76605400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr6:76592600-76624400	Weak transcription	Osteobl	bone
38	chr6:76592800-76606200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr6:76592800-76631800	Weak transcription	NHEK	skin
40	chr6:76593000-76603600	Weak transcription	Brain Hippocampus Middle	brain
41	chr6:76593000-76603800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr6:76593200-76606000	Weak transcription	HSMM	muscle
43	chr6:76593200-76606200	Weak transcription	NHDF-Ad	bronchial
44	chr6:76594400-76608400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr6:76594600-76632200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr6:76594800-76603200	Weak transcription	Liver	Liver
47	chr6:76597200-76603200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr6:76597200-76604000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr6:76597200-76608400	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr6:76597200-76624600	Weak transcription	Brain Angular Gyrus	brain

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