Variant report

Variant	rs12973258
Chromosome Location	chr19:19488718-19488719
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19475956..19479022-chr19:19487056..19489762,4	MCF-7	breast:
2	chr19:19485925..19490752-chr19:19494037..19501324,14	MCF-7	breast:
3	chr19:19488471..19489987-chr19:19516256..19519226,2	K562	blood:
4	chr19:19485973..19488912-chr19:19599291..19601456,3	MCF-7	breast:
5	chr19:19487332..19490283-chr19:19515104..19517573,4	MCF-7	breast:
6	chr19:19484073..19490340-chr19:19494015..19501154,14	MCF-7	breast:
7	chr19:19486238..19488843-chr19:19600330..19602869,2	MCF-7	breast:
8	chr19:19487435..19490372-chr19:19555512..19558220,2	MCF-7	breast:
9	chr19:19487227..19491094-chr19:19586686..19591214,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000167491	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs1000237	0.94[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs1009136	0.80[JPT][hapmap]
rs1010207	0.80[JPT][hapmap]
rs10282	0.94[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap]
rs10401193	0.89[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.85[ASN][1000 genomes]
rs10402308	0.82[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.87[TSI][hapmap]
rs10404728	0.85[ASN][1000 genomes]
rs10405625	0.82[ASN][1000 genomes]
rs10410664	0.82[ASN][1000 genomes]
rs10414830	0.94[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs10415849	0.89[ASW][hapmap];0.90[YRI][hapmap]
rs10419912	0.94[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap]
rs10422819	0.94[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap]
rs1054284	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1063966	0.94[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap]
rs11085259	0.88[CEU][hapmap]
rs11669516	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12972397	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12975119	0.82[ASN][1000 genomes]
rs12977524	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]
rs12983940	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1465695	0.85[ASN][1000 genomes]
rs1469712	0.94[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs1469713	0.94[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs17288409	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1858999	0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs1859287	0.88[CEU][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap]
rs2023883	0.88[CEU][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap]
rs2074301	0.82[CEU][hapmap];0.80[JPT][hapmap];0.86[MEX][hapmap]
rs2082421	0.85[ASN][1000 genomes]
rs2099333	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2099334	0.82[ASN][1000 genomes]
rs2163804	0.89[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2163805	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2285628	0.87[CEU][hapmap]
rs2288852	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs2301668	0.88[CEU][hapmap];0.86[MEX][hapmap]
rs2301786	0.80[JPT][hapmap]
rs2304098	0.94[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap]
rs2315025	0.80[JPT][hapmap]
rs2315279	0.90[ASN][1000 genomes]
rs2315281	0.88[ASN][1000 genomes]
rs2315610	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs28478453	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2905424	0.80[JPT][hapmap]
rs2905425	0.80[JPT][hapmap]
rs2905431	0.91[ASN][1000 genomes]
rs2905435	0.84[ASN][1000 genomes]
rs2916069	0.87[ASN][1000 genomes]
rs2916073	0.82[ASN][1000 genomes]
rs2916074	0.94[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs2916076	0.94[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs2965175	0.85[ASN][1000 genomes]
rs2965180	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs2965182	0.82[ASN][1000 genomes]
rs2965183	0.94[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs2965188	0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs2965189	0.94[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs2965198	0.80[JPT][hapmap]
rs34277109	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs34647936	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35418933	0.89[ASN][1000 genomes]
rs3752151	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3764567	0.84[JPT][hapmap]
rs3794990	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs3794993	0.94[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap]
rs4808194	0.88[CEU][hapmap]
rs4808196	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4808198	0.80[ASN][1000 genomes]
rs4808199	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];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4808200	0.94[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs4808202	0.82[ASN][1000 genomes]
rs4808203	0.94[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs4808208	0.94[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap]
rs4808950	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4808955	0.81[ASN][1000 genomes]
rs4808957	0.94[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs4808959	0.94[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs4808960	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4808961	0.94[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs4808964	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4808965	0.94[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap]
rs4808967	0.94[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap]
rs60003758	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60321073	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6511036	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6909	0.94[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap]
rs7245983	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs7250658	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7252888	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.85[ASN][1000 genomes]
rs7254230	0.80[JPT][hapmap]
rs7256149	0.83[ASN][1000 genomes]
rs7258508	0.85[EUR][1000 genomes]
rs7259434	0.88[CEU][hapmap];0.84[JPT][hapmap]
rs747050	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs754255	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs8105094	0.86[MEX][hapmap]
rs8105984	0.80[JPT][hapmap];0.86[MEX][hapmap]
rs8108647	0.88[CEU][hapmap];0.81[MEX][hapmap]
rs892021	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs892022	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs968525	0.88[CEU][hapmap];0.86[MEX][hapmap]
rs9917108	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911303	chr19:19256870-19505087	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	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
3	nsv1056419	chr19:19421218-19510611	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12973258	KIAA0892	cis	multi-tissue	Pritchard
rs12973258	FAM125A	cis	cerebellum	SCAN
rs12973258	ZNF826P	cis	cerebellum	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19478800-19495800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:19482600-19493200	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr19:19484200-19489000	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr19:19486400-19491800	Weak transcription	GM12878-XiMat	blood
5	chr19:19486400-19495400	Weak transcription	Primary B cells from peripheral blood	blood
6	chr19:19486400-19495600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr19:19488000-19489000	Enhancers	Fetal Lung	lung
8	chr19:19488000-19489000	Enhancers	Stomach Mucosa	stomach
9	chr19:19488000-19489200	Enhancers	Pancreas	Pancrea
10	chr19:19488000-19489200	Enhancers	Placenta Amnion	Placenta Amnion
11	chr19:19488000-19489200	Enhancers	HMEC	breast
12	chr19:19488000-19489600	Enhancers	K562	blood
13	chr19:19488000-19489800	Enhancers	Fetal Heart	heart
14	chr19:19488000-19490000	Enhancers	Colonic Mucosa	Colon
15	chr19:19488000-19490000	Enhancers	Lung	lung
16	chr19:19488200-19488800	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr19:19488200-19488800	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr19:19488200-19488800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
19	chr19:19488200-19489000	Enhancers	H1 Cell Line	embryonic stem cell
20	chr19:19488200-19489000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr19:19488200-19489000	Enhancers	Brain Angular Gyrus	brain
22	chr19:19488200-19489000	Enhancers	Right Ventricle	heart
23	chr19:19488200-19489000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr19:19488200-19489200	Enhancers	Spleen	Spleen
25	chr19:19488200-19489800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr19:19488200-19490000	Enhancers	Fetal Intestine Large	intestine
27	chr19:19488200-19492400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr19:19488400-19488800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr19:19488400-19488800	Enhancers	H9 Cell Line	embryonic stem cell
30	chr19:19488400-19488800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr19:19488400-19488800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr19:19488400-19488800	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr19:19488400-19488800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr19:19488400-19488800	Enhancers	Colon Smooth Muscle	Colon
35	chr19:19488400-19488800	Enhancers	Fetal Kidney	kidney
36	chr19:19488400-19488800	Enhancers	Fetal Muscle Leg	muscle
37	chr19:19488400-19488800	Enhancers	Gastric	stomach
38	chr19:19488400-19488800	Enhancers	Ovary	ovary
39	chr19:19488400-19488800	Flanking Active TSS	Rectal Smooth Muscle	rectum
40	chr19:19488400-19488800	Flanking Active TSS	HepG2	liver
41	chr19:19488400-19489000	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr19:19488400-19489000	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr19:19488400-19489000	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr19:19488400-19489000	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr19:19488400-19489000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr19:19488400-19489000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr19:19488400-19489000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr19:19488400-19489000	Enhancers	Adipose Nuclei	Adipose
49	chr19:19488400-19489000	Enhancers	Brain Anterior Caudate	brain
50	chr19:19488400-19489000	Flanking Active TSS	Brain Hippocampus Middle	brain

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