Variant report

Variant	rs12140446
Chromosome Location	chr1:94364559-94364560
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:94343372..94347640-chr1:94364498..94367458,3	K562	blood:
2	chr1:94342433..94344872-chr1:94364498..94367701,3	K562	blood:
3	chr1:94332093..94333597-chr1:94363497..94365167,2	K562	blood:
4	chr1:94363097..94365555-chr1:94372047..94374626,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000067334	Chromatin interaction
ENSG00000023909	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10489602	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10489603	0.93[GIH][hapmap]
rs10489604	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11165020	0.85[EUR][1000 genomes]
rs11165022	0.83[JPT][hapmap]
rs11165024	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11165026	0.83[JPT][hapmap]
rs12027630	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12040570	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12041975	0.83[JPT][hapmap]
rs12134359	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs12563731	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12565614	0.86[EUR][1000 genomes]
rs12565817	0.89[GIH][hapmap]
rs12566531	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12734571	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12739186	0.84[EUR][1000 genomes]
rs12752298	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1398798	0.96[CEU][hapmap];0.95[JPT][hapmap]
rs1884018	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1980083	0.81[CEU][hapmap]
rs2143992	0.83[JPT][hapmap]
rs2235971	0.86[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2391315	0.87[JPT][hapmap]
rs2391322	0.92[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs2747043	0.80[ASN][1000 genomes]
rs2747045	0.96[CEU][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2747046	1.00[YRI][hapmap]
rs2818169	0.81[ASN][1000 genomes]
rs3747965	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4075523	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs4141736	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4141737	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4240956	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs4350209	0.86[ASW][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap]
rs4847256	0.85[CEU][hapmap]
rs4847258	1.00[YRI][hapmap]
rs4847264	0.83[JPT][hapmap]
rs4847265	0.80[EUR][1000 genomes]
rs6663218	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs6664719	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6681265	0.82[JPT][hapmap]
rs7364910	0.86[EUR][1000 genomes]
rs743111	0.90[CHB][hapmap];0.82[JPT][hapmap]

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	nsv523355	chr1:94351328-94385591	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12140446	RP11-488P3.1	cis	Adipose Subcutaneous	GTEx
rs12140446	RP11-488P3.1	cis	Artery Tibial	GTEx
rs12140446	RP11-488P3.1	cis	Heart Left Ventricle	GTEx
rs12140446	RP11-488P3.1	cis	Muscle Skeletal	GTEx
rs12140446	RP11-488P3.1	cis	lung	GTEx
rs12140446	RP11-488P3.1	cis	Thyroid	GTEx
rs12140446	RP11-488P3.1	cis	Skin Sun Exposed Lower leg	GTEx
rs12140446	RP11-488P3.1	cis	Stomach	GTEx
rs12140446	RP11-488P3.1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94345000-94374200	Weak transcription	Gastric	stomach
2	chr1:94345000-94374200	Weak transcription	Spleen	Spleen
3	chr1:94345200-94374000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:94345200-94374200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:94345400-94369400	Weak transcription	Colonic Mucosa	Colon
6	chr1:94345400-94373200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr1:94345400-94373200	Weak transcription	Brain Substantia Nigra	brain
8	chr1:94345400-94373800	Weak transcription	Fetal Stomach	stomach
9	chr1:94345400-94374000	Weak transcription	Right Ventricle	heart
10	chr1:94345600-94369400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr1:94345600-94369400	Weak transcription	Fetal Lung	lung
12	chr1:94345600-94369800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr1:94345600-94371600	Weak transcription	Fetal Kidney	kidney
14	chr1:94345600-94373000	Weak transcription	Fetal Brain Female	brain
15	chr1:94345600-94373200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr1:94345600-94373200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:94345600-94373200	Weak transcription	Fetal Brain Male	brain
18	chr1:94345600-94373400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:94345600-94373400	Weak transcription	Psoas Muscle	Psoas
20	chr1:94345600-94373400	Weak transcription	Stomach Mucosa	stomach
21	chr1:94345600-94373600	Weak transcription	Brain Germinal Matrix	brain
22	chr1:94345800-94366000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr1:94345800-94369200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr1:94345800-94371200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:94347400-94374200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:94347600-94367600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:94350400-94367200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr1:94350600-94369400	Strong transcription	HMEC	breast
29	chr1:94351200-94364600	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr1:94351200-94367400	Strong transcription	Liver	Liver
31	chr1:94352800-94370400	Weak transcription	Lung	lung
32	chr1:94352800-94373000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:94353000-94367400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:94353600-94367200	Strong transcription	Osteobl	bone
35	chr1:94353600-94368200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr1:94353800-94367200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:94354200-94370400	Weak transcription	Small Intestine	intestine
38	chr1:94354200-94372600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr1:94354400-94367000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:94354600-94367000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr1:94354600-94373400	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr1:94356000-94367000	Strong transcription	Adipose Nuclei	Adipose
43	chr1:94356200-94367000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr1:94356600-94369400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:94356600-94372600	Weak transcription	Colon Smooth Muscle	Colon
46	chr1:94357200-94373800	Weak transcription	Thymus	Thymus
47	chr1:94357400-94374000	Weak transcription	Aorta	Aorta
48	chr1:94357600-94369400	Weak transcription	Primary T cells from cord blood	blood
49	chr1:94357600-94374200	Weak transcription	Pancreas	Pancrea
50	chr1:94357800-94373200	Weak transcription	Esophagus	oesophagus

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