Variant report

Variant	rs17185132
Chromosome Location	chr6:29759511-29759512
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:29755459..29758755-chr6:29758827..29760410,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZFP57-14	chr6:29758808-29760850	NONHSAT108552

Variant related genes	Relation type
ENSG00000181126	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs12660530	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12660712	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12660933	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12661487	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12662143	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12662144	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12662310	0.88[AFR][1000 genomes]
rs12662393	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12663821	0.88[AFR][1000 genomes]
rs12665210	0.84[AFR][1000 genomes]
rs12665345	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17178798	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17178917	0.81[AFR][1000 genomes]
rs17185181	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17185293	0.85[AFR][1000 genomes]
rs17185314	0.81[AFR][1000 genomes]
rs17185342	0.81[AFR][1000 genomes]
rs17185363	0.83[AFR][1000 genomes]
rs17875389	0.83[AFR][1000 genomes]
rs17875393	0.87[AFR][1000 genomes]
rs17875401	0.83[AFR][1000 genomes]
rs2394168	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2394169	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28372986	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28397055	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs28579685	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28634576	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3888577	0.90[AFR][1000 genomes]
rs56813912	0.90[AFR][1000 genomes]
rs57020131	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs57146053	0.83[AFR][1000 genomes]
rs57541649	0.90[AFR][1000 genomes]
rs58552394	0.90[AFR][1000 genomes]
rs59508891	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61276793	0.90[AFR][1000 genomes]
rs61729757	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61737605	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7740113	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7774397	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295811	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9295815	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9295816	0.90[AFR][1000 genomes]
rs9295817	0.90[AFR][1000 genomes]
rs9295818	0.90[AFR][1000 genomes]
rs9461551	0.88[AFR][1000 genomes]
rs9461552	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461553	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9461557	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461558	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461559	0.90[AFR][1000 genomes]
rs9461562	0.87[AFR][1000 genomes]
rs9461563	0.83[AFR][1000 genomes]
rs9468610	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468611	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9468612	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9468613	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9468616	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9468619	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9468620	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9468621	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9468622	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468623	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468624	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468626	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468627	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468629	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9468630	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9468632	0.90[AFR][1000 genomes]
rs9468638	0.83[AFR][1000 genomes]
rs9500844	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9500845	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9500846	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9500851	0.83[AFR][1000 genomes]
rs9500978	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9500979	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9500980	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9500982	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9500983	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9500987	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9500988	0.93[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs9500989	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9500990	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9500995	0.85[AFR][1000 genomes]
rs9500997	0.83[AFR][1000 genomes]
rs9501416	0.83[AFR][1000 genomes]
rs9501417	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv20940	chr6:29653954-29923410	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv428475	chr6:29659525-29763392	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv428139	chr6:29659525-29892317	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv427749	chr6:29659525-29975144	Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv508397	chr6:29663132-29761448	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	esv1794141	chr6:29670915-29765814	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	nsv10809	chr6:29692573-29794119	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv883532	chr6:29703262-29814963	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
9	esv3441842	chr6:29715749-29942950	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
10	esv11180	chr6:29729381-29800066	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	esv3332677	chr6:29733187-29961463	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
12	esv3423001	chr6:29733216-29878601	Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
13	esv3475027	chr6:29733297-29922699	Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
14	esv3475028	chr6:29733297-29922699	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
15	esv3420260	chr6:29734457-29835593	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
16	esv3330285	chr6:29736281-29881328	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
17	nsv883536	chr6:29746023-29760819	Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	nsv883537	chr6:29746023-29767611	Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	nsv883538	chr6:29748206-29760819	Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
20	nsv883539	chr6:29748206-29780529	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
21	esv3396224	chr6:29754243-29888093	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
22	nsv965702	chr6:29758408-29798943	Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29758400-29760000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr6:29758600-29759600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:29758600-29759800	Bivalent Enhancer	Stomach Mucosa	stomach
4	chr6:29758600-29760600	Active TSS	Placenta Amnion	Placenta Amnion
5	chr6:29758800-29759600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr6:29758800-29759600	Enhancers	Duodenum Mucosa	Duodenum
7	chr6:29758800-29759600	Flanking Active TSS	Hela-S3	cervix
8	chr6:29759000-29759600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr6:29759000-29759600	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr6:29759000-29759600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr6:29759000-29759600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr6:29759000-29759600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr6:29759000-29759800	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr6:29759000-29760600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr6:29759000-29760800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr6:29759000-29761000	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr6:29759200-29759600	Enhancers	Liver	Liver
18	chr6:29759200-29759800	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr6:29759200-29759800	Bivalent/Poised TSS	Monocytes-CD14+_RO01746	blood
20	chr6:29759200-29760000	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
21	chr6:29759200-29760800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr6:29759200-29760800	Active TSS	Brain Hippocampus Middle	brain
23	chr6:29759200-29760800	Active TSS	NHEK	skin
24	chr6:29759200-29761000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
25	chr6:29759200-29761000	Active TSS	Brain Angular Gyrus	brain
26	chr6:29759200-29761200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr6:29759400-29759600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
28	chr6:29759400-29759600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
29	chr6:29759400-29759600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
30	chr6:29759400-29759600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
31	chr6:29759400-29759600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
32	chr6:29759400-29759600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr6:29759400-29759600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr6:29759400-29759600	Flanking Active TSS	Esophagus	oesophagus
35	chr6:29759400-29759600	Active TSS	Pancreas	Pancrea
36	chr6:29759400-29759800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr6:29759400-29759800	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr6:29759400-29759800	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr6:29759400-29760000	Active TSS	HMEC	breast
40	chr6:29759400-29760400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr6:29759400-29760800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr6:29759400-29760800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr6:29759400-29760800	Active TSS	Brain Anterior Caudate	brain
44	chr6:29759400-29760800	Active TSS	Rectal Mucosa Donor 31	rectum
45	chr6:29759400-29761000	Active TSS	H9 Cell Line	embryonic stem cell
46	chr6:29759400-29761000	Active TSS	NHDF-Ad	bronchial

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