Variant report

Variant	rs12981965
Chromosome Location	chr19:37420793-37420794
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	chr19:37417109..37418736-chr19:37419934..37422422,2	MCF-7	breast:

Extended variants
information (count: 102 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10401212	1.00[JPT][hapmap]
rs10401417	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10404981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10405238	0.86[ASN][1000 genomes]
rs10405984	0.83[CHB][hapmap]
rs10407557	0.85[ASN][1000 genomes]
rs10407712	0.90[ASN][1000 genomes]
rs10408534	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10408951	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10409206	0.96[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10410594	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10411251	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10411931	0.81[CEU][hapmap];0.82[CHB][hapmap]
rs10412863	0.90[ASN][1000 genomes]
rs10414781	0.83[ASN][1000 genomes]
rs10414907	0.85[ASN][1000 genomes]
rs10416960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10418144	0.85[ASN][1000 genomes]
rs10418176	0.81[JPT][hapmap]
rs10420859	0.90[ASN][1000 genomes]
rs10424100	0.86[ASN][1000 genomes]
rs11084868	0.85[ASN][1000 genomes]
rs12710052	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12977971	0.81[AFR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13345230	0.80[ASN][1000 genomes]
rs13345489	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1551025	0.90[ASN][1000 genomes]
rs1623097	0.90[ASN][1000 genomes]
rs1623796	0.91[JPT][hapmap]
rs1624293	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1644664	0.88[ASN][1000 genomes]
rs1644701	0.83[ASN][1000 genomes]
rs1667351	0.92[JPT][hapmap]
rs1667357	0.86[ASN][1000 genomes]
rs1667359	0.86[ASN][1000 genomes]
rs16971771	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs16971772	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs16971850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17639910	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17707101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2010342	0.85[ASN][1000 genomes]
rs2595552	0.86[ASN][1000 genomes]
rs28412852	0.84[AFR][1000 genomes]
rs28495495	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28542490	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28555503	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28608841	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28626335	0.85[ASN][1000 genomes]
rs28655720	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34791663	0.90[ASN][1000 genomes]
rs35881914	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3816390	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3816391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3955478	1.00[JPT][hapmap]
rs4006391	0.85[ASN][1000 genomes]
rs4006392	0.85[ASN][1000 genomes]
rs4805189	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4805190	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4806376	0.91[ASN][1000 genomes]
rs4806377	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4806380	0.81[CEU][hapmap];0.82[CHB][hapmap]
rs4806386	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs543518	0.92[JPT][hapmap]
rs56387564	0.85[ASN][1000 genomes]
rs60293110	0.85[ASN][1000 genomes]
rs62113193	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62115573	0.85[ASN][1000 genomes]
rs62115574	0.85[ASN][1000 genomes]
rs62115612	0.91[ASN][1000 genomes]
rs62115615	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6510572	0.87[AFR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71266562	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs71356024	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7249013	0.95[ASN][1000 genomes]
rs7250498	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7251087	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7252797	0.86[ASN][1000 genomes]
rs7257045	0.83[ASN][1000 genomes]
rs7257484	0.83[ASN][1000 genomes]
rs73626774	0.85[ASN][1000 genomes]
rs8101062	0.85[AFR][1000 genomes]
rs8101922	0.85[ASN][1000 genomes]
rs8112709	0.84[EUR][1000 genomes]
rs826263	0.85[JPT][hapmap]
rs9304878	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs997516	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers 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	61 gene(s)	inside rSNPs	diseases
4	nsv529817	chr19:36930549-37654062	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription 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	73 gene(s)	inside rSNPs	diseases
6	nsv521605	chr19:37261810-37483444	ZNF genes & repeats Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv1060155	chr19:37274915-37458788	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv544000	chr19:37274915-37458788	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	esv3507199	chr19:37284708-37805639	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers 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	27 gene(s)	inside rSNPs	diseases
10	esv3507200	chr19:37284708-37805639	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers 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	27 gene(s)	inside rSNPs	diseases
11	esv3497360	chr19:37290273-37745365	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
12	esv3497361	chr19:37290273-37745365	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
13	nsv911651	chr19:37300554-37428465	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
14	nsv458568	chr19:37325826-37747108	Strong transcription ZNF genes & repeats Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
15	nsv579461	chr19:37325826-37747108	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
16	nsv523848	chr19:37357289-37487632	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37408200-37436400	Weak transcription	Fetal Thymus	thymus
2	chr19:37408200-37440600	Weak transcription	Stomach Mucosa	stomach
3	chr19:37408400-37440600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr19:37408600-37439600	Weak transcription	Fetal Heart	heart
5	chr19:37409000-37444800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:37409000-37447400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr19:37409600-37423600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr19:37409800-37421400	Weak transcription	Fetal Brain Male	brain
9	chr19:37410600-37427600	Weak transcription	NH-A	brain
10	chr19:37413600-37421400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr19:37413600-37427600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr19:37413800-37421400	Weak transcription	Brain Hippocampus Middle	brain
13	chr19:37413800-37421800	Weak transcription	Colonic Mucosa	Colon
14	chr19:37413800-37421800	Weak transcription	Esophagus	oesophagus
15	chr19:37413800-37421800	Weak transcription	Fetal Intestine Large	intestine
16	chr19:37413800-37422000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr19:37413800-37422000	Weak transcription	Gastric	stomach
18	chr19:37413800-37422000	Weak transcription	Thymus	Thymus
19	chr19:37413800-37427400	Weak transcription	Right Ventricle	heart
20	chr19:37413800-37427600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr19:37413800-37427800	Weak transcription	HSMMtube	muscle
22	chr19:37413800-37428000	Weak transcription	HUVEC	blood vessel
23	chr19:37414000-37421600	Weak transcription	Fetal Brain Female	brain
24	chr19:37414400-37421800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr19:37414800-37421800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr19:37415000-37421600	Weak transcription	Colon Smooth Muscle	Colon
27	chr19:37415800-37444600	ZNF genes & repeats	Liver	Liver
28	chr19:37416200-37421800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr19:37416200-37427800	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr19:37417400-37421200	Weak transcription	Fetal Muscle Leg	muscle
31	chr19:37417400-37421400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr19:37417400-37421400	Weak transcription	Osteobl	bone
33	chr19:37417400-37421600	Weak transcription	Fetal Muscle Trunk	muscle
34	chr19:37417400-37422000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr19:37417600-37421600	Weak transcription	Primary B cells from cord blood	blood
36	chr19:37417600-37421600	Weak transcription	Brain Angular Gyrus	brain
37	chr19:37417600-37421800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr19:37417600-37422000	Weak transcription	Brain Cingulate Gyrus	brain
39	chr19:37417800-37421600	Weak transcription	Stomach Smooth Muscle	stomach
40	chr19:37417800-37421800	Weak transcription	Placenta	Placenta
41	chr19:37417800-37421800	Weak transcription	Psoas Muscle	Psoas
42	chr19:37417800-37422000	Weak transcription	Brain Germinal Matrix	brain
43	chr19:37418000-37421600	Weak transcription	Brain Anterior Caudate	brain
44	chr19:37418000-37421600	Weak transcription	Brain Substantia Nigra	brain
45	chr19:37418000-37421600	Weak transcription	Dnd41	blood
46	chr19:37418000-37422000	Weak transcription	NHDF-Ad	bronchial
47	chr19:37418000-37422200	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr19:37418400-37421400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr19:37418400-37421600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr19:37418400-37421800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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