Variant report

Variant	rs12977524
Chromosome Location	chr19:19568244-19568245
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:19567763-19568321	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:19514082..19516953-chr19:19567668..19570496,2	K562	blood:

Variant related genes	Relation type
GATAD2A	TF binding region
ENSG00000167491	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs1000237	0.94[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs1009136	0.80[JPT][hapmap]
rs1010207	0.80[JPT][hapmap]
rs10282	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs10401193	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10402308	0.93[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs10402451	0.87[ASN][1000 genomes]
rs10402627	0.85[ASN][1000 genomes]
rs10404728	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10405625	0.91[ASN][1000 genomes]
rs10410664	0.91[ASN][1000 genomes]
rs10414830	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs10419912	0.94[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs10422819	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs1047361	0.87[ASN][1000 genomes]
rs1054284	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1054930	0.81[ASN][1000 genomes]
rs1063966	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs11085259	1.00[CEU][hapmap]
rs11669516	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12972397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12973258	0.89[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12975119	0.91[ASN][1000 genomes]
rs12981405	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12983940	0.91[AMR][1000 genomes]
rs1465695	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1469712	0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs1469713	0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs16996148	0.89[ASW][hapmap];0.90[LWK][hapmap];0.93[YRI][hapmap]
rs17288409	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1808653	0.87[ASN][1000 genomes]
rs1858999	0.94[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs1859287	1.00[CEU][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap]
rs1865034	0.87[ASN][1000 genomes]
rs2023883	1.00[CEU][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs2074301	0.93[CEU][hapmap];0.80[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap]
rs2082421	0.95[ASN][1000 genomes]
rs2099333	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2099334	0.91[ASN][1000 genomes]
rs2163804	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2163805	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2285628	1.00[CEU][hapmap]
rs2288852	0.94[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs2301668	1.00[CEU][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap]
rs2301786	0.80[JPT][hapmap]
rs2304098	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs2315025	0.80[JPT][hapmap]
rs2315279	0.81[ASN][1000 genomes]
rs2315610	0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs28478453	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2905424	0.80[JPT][hapmap]
rs2905425	0.80[JPT][hapmap]
rs2905431	0.81[ASN][1000 genomes]
rs2916069	0.84[ASN][1000 genomes]
rs2916073	0.91[ASN][1000 genomes]
rs2916074	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs2916076	0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs2965180	0.94[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs2965182	0.91[ASN][1000 genomes]
rs2965183	0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs2965188	0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs2965189	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs2965198	0.80[JPT][hapmap]
rs34277109	0.94[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs34647936	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35418933	0.80[ASN][1000 genomes]
rs3752151	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3764567	0.84[JPT][hapmap]
rs3794990	0.94[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs3794993	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs4808194	1.00[CEU][hapmap]
rs4808196	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4808198	0.90[ASN][1000 genomes]
rs4808199	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808200	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs4808202	0.91[ASN][1000 genomes]
rs4808203	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs4808208	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap]
rs4808950	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4808955	0.90[ASN][1000 genomes]
rs4808957	0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs4808959	0.94[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs4808960	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808961	0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs4808964	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4808965	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs4808967	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs60003758	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60321073	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6511036	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6511038	0.85[ASN][1000 genomes]
rs6909	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs7245983	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs7250658	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7250893	0.84[ASN][1000 genomes]
rs7252888	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7253807	0.82[ASN][1000 genomes]
rs7254230	0.80[JPT][hapmap]
rs7256149	0.93[ASN][1000 genomes]
rs7258508	0.80[EUR][1000 genomes]
rs7259434	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs747050	0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs751856	0.87[ASN][1000 genomes]
rs751858	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs754255	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8105094	0.95[MEX][hapmap];0.82[TSI][hapmap]
rs8105984	0.87[CEU][hapmap];0.80[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap]
rs8108647	1.00[CEU][hapmap];0.91[MEX][hapmap]
rs892021	0.94[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs892022	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs968525	1.00[CEU][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap]
rs9917108	0.90[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12977524	ZNF826P	cis	cerebellum	SCAN
rs12977524	KIAA0892	cis	multi-tissue	Pritchard
rs12977524	ZNF714	cis	parietal	SCAN
rs12977524	EPS15L1	cis	cerebellum	SCAN
rs12977524	FAM125A	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19545600-19568600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr19:19545800-19568600	Weak transcription	Brain Substantia Nigra	brain
3	chr19:19545800-19570600	Weak transcription	Brain Cingulate Gyrus	brain
4	chr19:19546200-19569000	Weak transcription	Colon Smooth Muscle	Colon
5	chr19:19551000-19571200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr19:19557600-19568600	Weak transcription	HUVEC	blood vessel
7	chr19:19557600-19569000	Weak transcription	NH-A	brain
8	chr19:19557800-19569400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr19:19558200-19571400	Weak transcription	Brain Germinal Matrix	brain
10	chr19:19558400-19568600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr19:19558600-19570400	Weak transcription	HMEC	breast
12	chr19:19558800-19568800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr19:19558800-19569600	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr19:19559000-19568600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr19:19559000-19569200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr19:19559200-19570600	Weak transcription	Fetal Brain Female	brain
17	chr19:19559400-19568600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr19:19559400-19569000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr19:19560200-19568600	Weak transcription	Psoas Muscle	Psoas
20	chr19:19561400-19568600	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr19:19561400-19569600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr19:19561400-19570600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr19:19562600-19570400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr19:19562800-19568600	Weak transcription	Brain Hippocampus Middle	brain
25	chr19:19562800-19570200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr19:19562800-19570400	Weak transcription	Brain Angular Gyrus	brain
27	chr19:19563000-19570200	Weak transcription	Fetal Heart	heart
28	chr19:19563400-19570600	Weak transcription	A549	lung
29	chr19:19563600-19568800	Weak transcription	Brain Anterior Caudate	brain
30	chr19:19563600-19569000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr19:19563800-19569000	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr19:19563800-19570400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr19:19564000-19568600	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr19:19564000-19568600	Weak transcription	Fetal Lung	lung
35	chr19:19564000-19568600	Weak transcription	Right Atrium	heart
36	chr19:19564000-19568600	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr19:19564000-19568800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr19:19564200-19568600	Weak transcription	Liver	Liver
39	chr19:19564200-19568600	Weak transcription	Stomach Mucosa	stomach
40	chr19:19564200-19568800	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr19:19564400-19568600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr19:19564400-19568600	Weak transcription	Primary hematopoietic stem cells	blood
43	chr19:19564400-19568600	Weak transcription	Adipose Nuclei	Adipose
44	chr19:19564400-19569000	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr19:19564400-19569200	Weak transcription	Rectal Smooth Muscle	rectum
46	chr19:19564400-19571800	Weak transcription	Fetal Kidney	kidney
47	chr19:19565200-19569800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr19:19565400-19569400	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr19:19565600-19568600	Weak transcription	Colonic Mucosa	Colon
50	chr19:19565600-19570200	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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