Variant report

Variant	rs12489511
Chromosome Location	chr3:121513185-121513186
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:121466861..121468616-chr3:121512374..121514092,2	K562	blood:

Variant related genes	Relation type
ENSG00000173230	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10934560	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12490565	0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12492973	0.80[AMR][1000 genomes]
rs13067629	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1492177	0.83[CHB][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs1574655	0.80[EUR][1000 genomes]
rs1574735	0.80[EUR][1000 genomes]
rs17849995	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1873645	0.92[CHB][hapmap]
rs1919552	1.00[CHB][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap]
rs1919557	1.00[CHB][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs1920294	0.80[AMR][1000 genomes]
rs2001390	0.80[EUR][1000 genomes]
rs2001391	1.00[CHB][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs2070179	0.92[CHB][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]
rs2141614	0.90[JPT][hapmap]
rs2331963	0.83[MEX][hapmap];0.80[AMR][1000 genomes]
rs2332056	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.84[TSI][hapmap];0.82[ASN][1000 genomes]
rs2840143	0.83[CHB][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs34920680	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34980632	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35713885	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36022362	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3817599	0.84[GIH][hapmap]
rs4259001	0.80[AMR][1000 genomes]
rs4482697	0.83[MEX][hapmap];0.80[AMR][1000 genomes]
rs4505751	0.80[AMR][1000 genomes]
rs4676690	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4676751	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4676754	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57420306	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59740137	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62268808	0.80[AMR][1000 genomes]
rs6438660	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6438661	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6770719	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6771716	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6774164	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6776596	0.80[AMR][1000 genomes]
rs6776703	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6791510	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6794341	0.80[EUR][1000 genomes]
rs6802033	0.92[CHB][hapmap]
rs6803839	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs6807711	1.00[CHB][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs73179983	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73181839	0.82[ASN][1000 genomes]
rs7375038	0.92[CHB][hapmap];0.89[GIH][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]
rs7429247	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs7611913	0.92[CHB][hapmap]
rs7646346	1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7646585	1.00[CHB][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs7652239	0.82[ASN][1000 genomes]
rs9289172	0.92[CHB][hapmap]
rs9289173	0.92[CHB][hapmap]
rs953730	0.80[GIH][hapmap]
rs9681049	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9681209	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9809114	0.92[CHB][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]
rs9812411	0.84[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs9829053	0.81[EUR][1000 genomes]
rs9832267	0.80[EUR][1000 genomes]
rs9835182	0.80[EUR][1000 genomes]
rs9854052	0.80[EUR][1000 genomes]
rs9864907	1.00[CHB][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]
rs9876021	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591396	chr3:120970900-121557533	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats 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	50 gene(s)	inside rSNPs	diseases
2	nsv432480	chr3:121355723-121629928	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS 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	39 gene(s)	inside rSNPs	diseases
3	nsv432482	chr3:121364236-121629634	Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv432481	chr3:121364236-121637178	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking 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	40 gene(s)	inside rSNPs	diseases
5	nsv829703	chr3:121383290-121534493	Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	nsv516233	chr3:121419301-121670405	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv877383	chr3:121465220-121650736	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv432483	chr3:121488995-121629634	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats 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	8 gene(s)	inside rSNPs	diseases
9	esv33139	chr3:121500400-122091831	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12489511	ADPRH	cis	parietal	SCAN
rs12489511	EAF2	Cis_1M	lymphoblastoid	RTeQTL
rs12489511	ILDR1	cis	lymphoblastoid	seeQTL
rs12489511	SLC15A2	cis	cerebellum	SCAN
rs12489511	EAF2	cis	lymphoblastoid	seeQTL
rs12489511	SLC15A2	cis	parietal	SCAN
rs12489511	HCLS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121486200-121526600	Weak transcription	Stomach Mucosa	stomach
2	chr3:121486800-121532200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:121487800-121516400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr3:121487800-121519000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr3:121488600-121517800	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr3:121489800-121514800	Weak transcription	Small Intestine	intestine
7	chr3:121489800-121529800	Weak transcription	Aorta	Aorta
8	chr3:121490000-121529800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:121490000-121529800	Weak transcription	Pancreas	Pancrea
10	chr3:121491600-121552600	Weak transcription	NHLF	lung
11	chr3:121494200-121544200	Weak transcription	Fetal Brain Male	brain
12	chr3:121494400-121518800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:121494400-121530000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:121494800-121516000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr3:121500200-121515800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr3:121500200-121524200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr3:121500200-121541400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr3:121500600-121528200	Weak transcription	Brain Angular Gyrus	brain
19	chr3:121501200-121524000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr3:121501400-121529800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:121504800-121524000	Weak transcription	Hela-S3	cervix
22	chr3:121505000-121521400	Weak transcription	Fetal Intestine Small	intestine
23	chr3:121505800-121523600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr3:121506400-121529800	Weak transcription	Fetal Stomach	stomach
25	chr3:121507000-121529800	Weak transcription	Colonic Mucosa	Colon
26	chr3:121507000-121545400	Weak transcription	Fetal Heart	heart
27	chr3:121507200-121536000	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr3:121508000-121523600	Weak transcription	Fetal Brain Female	brain
29	chr3:121508000-121525000	Weak transcription	Thymus	Thymus
30	chr3:121508000-121529800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr3:121508200-121535800	Weak transcription	Psoas Muscle	Psoas
32	chr3:121508400-121518000	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr3:121508400-121523200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr3:121508400-121524400	Weak transcription	Left Ventricle	heart
35	chr3:121508400-121524400	Weak transcription	Lung	lung
36	chr3:121508400-121529800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr3:121508400-121529800	Weak transcription	Esophagus	oesophagus
38	chr3:121508400-121536400	Weak transcription	HUVEC	blood vessel
39	chr3:121508600-121523400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr3:121508600-121523400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr3:121508600-121523600	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr3:121508600-121524800	Weak transcription	Colon Smooth Muscle	Colon
43	chr3:121508600-121525000	Weak transcription	Brain Anterior Caudate	brain
44	chr3:121508600-121529600	Weak transcription	Brain Substantia Nigra	brain
45	chr3:121508600-121529800	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr3:121508600-121529800	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr3:121508600-121529800	Weak transcription	NHEK	skin
48	chr3:121508600-121541400	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr3:121508800-121513400	Weak transcription	NHDF-Ad	bronchial
50	chr3:121508800-121515200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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