Variant report

Variant	rs12610750
Chromosome Location	chr19:21130283-21130284
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:21124387..21126595-chr19:21129898..21132890,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10416168	0.88[EUR][1000 genomes]
rs10422656	0.88[EUR][1000 genomes]
rs11085394	0.82[ASN][1000 genomes]
rs11665919	0.84[ASN][1000 genomes]
rs11667236	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11669368	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11670561	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12459111	0.81[ASN][1000 genomes]
rs12459251	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12609663	0.88[ASN][1000 genomes]
rs12610256	0.83[EUR][1000 genomes]
rs12611073	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12971543	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12971562	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12978510	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12981899	0.86[ASN][1000 genomes]
rs12983551	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1985021	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2081049	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35787677	0.92[ASN][1000 genomes]
rs35932444	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3867196	0.84[ASN][1000 genomes]
rs4305208	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56397942	0.83[ASN][1000 genomes]
rs62123243	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72282090	0.82[ASN][1000 genomes]
rs7246544	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7249876	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7251344	0.96[ASN][1000 genomes]
rs7257679	0.89[EUR][1000 genomes]
rs8101800	0.81[EUR][1000 genomes]
rs8103666	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8103964	0.88[EUR][1000 genomes]
rs8104353	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8104485	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8107262	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8107954	0.88[ASN][1000 genomes]
rs8109293	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752729	chr19:20818886-21169554	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1062776	chr19:20818886-21273361	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv932110	chr19:20818886-21278952	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	esv2763043	chr19:20818886-21290543	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv1063954	chr19:21000562-21177577	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv578946	chr19:21014403-21151796	ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	esv3385528	chr19:21030777-21495566	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv817536	chr19:21041855-21348237	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription ZNF genes & repeats Flanking 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 miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv1067455	chr19:21053665-21141787	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
10	esv1850387	chr19:21109758-21294264	Active TSS ZNF genes & repeats Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
11	nsv1066170	chr19:21114796-21142630	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12610750	ZNF85	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21106800-21131000	Weak transcription	Gastric	stomach
2	chr19:21107000-21133200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:21107200-21132600	Weak transcription	Brain Hippocampus Middle	brain
4	chr19:21107200-21133800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:21107400-21131600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr19:21107600-21133400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr19:21111800-21131000	Weak transcription	NH-A	brain
8	chr19:21114400-21132800	Weak transcription	Colon Smooth Muscle	Colon
9	chr19:21116600-21133400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr19:21118400-21131600	Weak transcription	Fetal Thymus	thymus
11	chr19:21120000-21133200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr19:21121200-21130400	Weak transcription	Pancreas	Pancrea
13	chr19:21122200-21133400	Weak transcription	Brain Substantia Nigra	brain
14	chr19:21125600-21134000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
15	chr19:21125600-21134200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr19:21125800-21131600	Weak transcription	Fetal Heart	heart
17	chr19:21126000-21133000	ZNF genes & repeats	Dnd41	blood
18	chr19:21126400-21131200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr19:21126400-21131200	Weak transcription	Fetal Intestine Large	intestine
20	chr19:21126400-21131400	Weak transcription	HSMMtube	muscle
21	chr19:21126400-21133000	Weak transcription	Ovary	ovary
22	chr19:21126400-21133200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr19:21126400-21133600	Weak transcription	Left Ventricle	heart
24	chr19:21126600-21131000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr19:21126600-21131400	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr19:21126600-21133600	Weak transcription	Thymus	Thymus
27	chr19:21127000-21133000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
28	chr19:21127000-21133400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
29	chr19:21127200-21132200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr19:21128000-21131200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr19:21128000-21133000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr19:21128400-21130800	Weak transcription	Fetal Muscle Leg	muscle
33	chr19:21128400-21130800	Weak transcription	NHDF-Ad	bronchial
34	chr19:21128400-21131000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr19:21128600-21132600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr19:21128600-21133600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr19:21128800-21130400	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr19:21128800-21130800	Weak transcription	Primary B cells from peripheral blood	blood
39	chr19:21128800-21130800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr19:21128800-21131000	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr19:21128800-21131000	Weak transcription	Brain Germinal Matrix	brain
42	chr19:21128800-21131000	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr19:21128800-21131000	Weak transcription	Osteobl	bone
44	chr19:21128800-21131200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr19:21128800-21132600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr19:21128800-21133400	Weak transcription	Placenta	Placenta
47	chr19:21128800-21133600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr19:21129000-21130800	Weak transcription	Primary hematopoietic stem cells	blood
49	chr19:21129000-21130800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr19:21129000-21130800	Weak transcription	Rectal Mucosa Donor 29	rectum

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