Variant report

Variant	rs12972502
Chromosome Location	chr19:21131728-21131729
allele	A/G/T
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: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10500214	0.94[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12151124	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12973946	0.96[EUR][1000 genomes]
rs12974516	0.94[EUR][1000 genomes]
rs12976498	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12977377	0.94[EUR][1000 genomes]
rs12978422	0.94[EUR][1000 genomes]
rs12979034	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12980702	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12982799	0.84[EUR][1000 genomes]
rs12984683	0.84[EUR][1000 genomes]
rs12985632	0.96[EUR][1000 genomes]
rs12985960	0.94[CEU][hapmap]
rs34083865	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34094278	0.83[EUR][1000 genomes]
rs34147545	0.96[EUR][1000 genomes]
rs34319995	0.98[EUR][1000 genomes]
rs34353115	0.94[EUR][1000 genomes]
rs34364519	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34428650	0.83[EUR][1000 genomes]
rs34570925	0.96[EUR][1000 genomes]
rs34624594	0.83[EUR][1000 genomes]
rs34655445	0.84[EUR][1000 genomes]
rs34810042	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35087386	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35142954	0.96[EUR][1000 genomes]
rs35301331	0.94[EUR][1000 genomes]
rs35355399	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35356210	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35629911	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35646729	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35713135	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35713726	0.84[EUR][1000 genomes]
rs35739003	0.84[EUR][1000 genomes]
rs35748394	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35775609	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35807371	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35816744	0.94[EUR][1000 genomes]
rs35891780	0.93[EUR][1000 genomes]
rs35908447	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35992021	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs36066016	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36116339	0.81[EUR][1000 genomes]
rs3853666	0.81[EUR][1000 genomes]
rs3853667	0.81[EUR][1000 genomes]
rs66746089	0.84[EUR][1000 genomes]
rs66886362	0.96[EUR][1000 genomes]
rs66889224	0.94[EUR][1000 genomes]
rs67084493	0.96[EUR][1000 genomes]
rs67242454	0.94[EUR][1000 genomes]
rs67493653	0.98[EUR][1000 genomes]
rs68066643	0.94[EUR][1000 genomes]
rs68101689	0.86[EUR][1000 genomes]
rs68140009	0.94[EUR][1000 genomes]
rs7254676	0.94[EUR][1000 genomes]
rs73005097	0.94[EUR][1000 genomes]
rs73007025	0.94[EUR][1000 genomes]
rs73007030	0.94[EUR][1000 genomes]
rs73007042	0.94[EUR][1000 genomes]
rs74182996	0.84[EUR][1000 genomes]
rs74182998	0.83[EUR][1000 genomes]
rs74182999	0.84[EUR][1000 genomes]
rs74183002	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8100072	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8113635	0.81[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][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

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21107000-21133200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:21107200-21132600	Weak transcription	Brain Hippocampus Middle	brain
3	chr19:21107200-21133800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:21107600-21133400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:21114400-21132800	Weak transcription	Colon Smooth Muscle	Colon
6	chr19:21116600-21133400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr19:21120000-21133200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr19:21122200-21133400	Weak transcription	Brain Substantia Nigra	brain
9	chr19:21125600-21134000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
10	chr19:21125600-21134200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr19:21126000-21133000	ZNF genes & repeats	Dnd41	blood
12	chr19:21126400-21133000	Weak transcription	Ovary	ovary
13	chr19:21126400-21133200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr19:21126400-21133600	Weak transcription	Left Ventricle	heart
15	chr19:21126600-21133600	Weak transcription	Thymus	Thymus
16	chr19:21127000-21133000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
17	chr19:21127000-21133400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
18	chr19:21127200-21132200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr19:21128000-21133000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr19:21128600-21132600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr19:21128600-21133600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr19:21128800-21132600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr19:21128800-21133400	Weak transcription	Placenta	Placenta
24	chr19:21128800-21133600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr19:21129800-21133200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr19:21129800-21133600	Weak transcription	Fetal Brain Male	brain
27	chr19:21130000-21133000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr19:21130400-21132400	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
29	chr19:21130400-21133000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
30	chr19:21130800-21131800	ZNF genes & repeats	NHDF-Ad	bronchial
31	chr19:21130800-21132200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr19:21130800-21132400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
33	chr19:21130800-21132400	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
34	chr19:21130800-21132400	ZNF genes & repeats	Fetal Lung	lung
35	chr19:21130800-21132800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr19:21130800-21132800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
37	chr19:21130800-21132800	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
38	chr19:21130800-21133000	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
39	chr19:21130800-21133000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
40	chr19:21130800-21133000	ZNF genes & repeats	Adipose Nuclei	Adipose
41	chr19:21130800-21133400	Strong transcription	HSMM	muscle
42	chr19:21130800-21133800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr19:21130800-21134800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
44	chr19:21131000-21132000	ZNF genes & repeats	Osteobl	bone
45	chr19:21131000-21132200	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
46	chr19:21131000-21132200	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
47	chr19:21131000-21132200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
48	chr19:21131000-21132200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
49	chr19:21131000-21132400	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr19:21131000-21132400	ZNF genes & repeats	Brain Germinal Matrix	brain

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