Variant report

Variant	rs12495230
Chromosome Location	chr3:70049499-70049500
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:69743330..69744905-chr3:70049287..70050873,2	K562	blood:
2	chr3:69911868..69913923-chr3:70048911..70050413,2	K562	blood:
3	chr3:69370120..69372204-chr3:70049315..70051273,2	K562	blood:

Variant related genes	Relation type
ENSG00000114541	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1021413	0.88[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs1027233	0.85[AMR][1000 genomes]
rs1027234	0.80[AMR][1000 genomes]
rs1157456	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11718882	0.82[ASN][1000 genomes]
rs11923682	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11926368	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1388649	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1491686	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1491687	0.81[ASN][1000 genomes]
rs1491688	0.82[ASN][1000 genomes]
rs1491689	0.81[ASN][1000 genomes]
rs1491695	1.00[ASW][hapmap];0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.82[TSI][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1491698	0.92[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1492055	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1492056	0.85[AMR][1000 genomes]
rs1546075	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17727959	0.87[ASN][1000 genomes]
rs1844877	0.82[ASN][1000 genomes]
rs1873583	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1873584	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1907646	0.82[ASN][1000 genomes]
rs2131026	0.82[ASN][1000 genomes]
rs2131122	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2172211	0.84[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs28524674	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34790356	0.84[ASN][1000 genomes]
rs35180789	0.88[ASN][1000 genomes]
rs35416604	0.82[ASN][1000 genomes]
rs36125122	0.82[ASN][1000 genomes]
rs3772111	0.81[ASN][1000 genomes]
rs3821364	0.84[CHB][hapmap];0.80[CHD][hapmap];0.94[JPT][hapmap]
rs3849467	0.80[AMR][1000 genomes]
rs3967688	0.86[ASN][1000 genomes]
rs4855331	0.82[ASN][1000 genomes]
rs4855453	0.88[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs4855454	0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs4855455	0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs4855456	0.82[ASN][1000 genomes]
rs55842620	0.82[ASN][1000 genomes]
rs56351003	0.88[ASN][1000 genomes]
rs576	0.83[CHD][hapmap]
rs6549254	0.82[ASN][1000 genomes]
rs6549256	0.80[ASN][1000 genomes]
rs6549257	0.83[ASN][1000 genomes]
rs6549258	0.83[ASN][1000 genomes]
rs6549259	0.83[ASN][1000 genomes]
rs6549260	0.86[ASN][1000 genomes]
rs6549261	0.92[CEU][hapmap];0.84[CHB][hapmap];0.86[CHD][hapmap];0.80[JPT][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6549262	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6549264	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6549265	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6549266	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6771970	0.82[ASN][1000 genomes]
rs6772684	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6784666	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6809508	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs704246	0.96[CHD][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs73119519	0.82[ASN][1000 genomes]
rs7429562	0.82[ASN][1000 genomes]
rs7431913	0.83[ASN][1000 genomes]
rs7619924	0.81[AMR][1000 genomes]
rs7634340	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7634564	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7647661	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs902711	0.88[ASN][1000 genomes]
rs902712	0.88[ASN][1000 genomes]
rs923702	0.83[ASN][1000 genomes]
rs9310178	0.92[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9310179	0.81[ASW][hapmap];0.92[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9310180	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs956436	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9809122	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9815287	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9818798	0.81[AMR][1000 genomes]
rs9826811	0.82[AMR][1000 genomes]
rs9834141	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9839734	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9840397	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9840590	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9843867	0.81[AMR][1000 genomes]
rs9849031	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9851891	0.96[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9863457	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9868203	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[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	nsv533396	chr3:69964029-70538306	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12495230	RP11-460N16.1	cis	Artery Aorta	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:70041200-70061000	Weak transcription	Aorta	Aorta
2	chr3:70045800-70049600	Enhancers	Fetal Lung	lung
3	chr3:70045800-70050400	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr3:70045800-70050600	Enhancers	Fetal Stomach	stomach
5	chr3:70047200-70050800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:70047600-70049600	Weak transcription	Brain Germinal Matrix	brain
7	chr3:70048000-70050400	Active TSS	K562	blood
8	chr3:70048000-70051200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr3:70048200-70050800	Active TSS	Brain Anterior Caudate	brain
10	chr3:70048600-70050600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:70048800-70049800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:70049000-70049600	Weak transcription	A549	lung
13	chr3:70049000-70049800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr3:70049000-70049800	Active TSS	Duodenum Mucosa	Duodenum
15	chr3:70049000-70050000	Enhancers	Stomach Smooth Muscle	stomach
16	chr3:70049000-70050200	Active TSS	Brain Hippocampus Middle	brain
17	chr3:70049000-70050400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:70049000-70050800	Weak transcription	Brain Angular Gyrus	brain
19	chr3:70049200-70050200	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr3:70049200-70051400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:70049400-70050000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr3:70049400-70050000	Weak transcription	Brain Substantia Nigra	brain
23	chr3:70049400-70050000	Active TSS	Ovary	ovary
24	chr3:70049400-70050200	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr3:70049400-70050400	Weak transcription	Brain Cingulate Gyrus	brain

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