Variant report

Variant	rs12711786
Chromosome Location	chr2:114516985-114516986
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:114512582..114515674-chr2:114516372..114520568,3	MCF-7	breast:
2	chr2:114514472..114517401-chr2:114595773..114597784,2	MCF-7	breast:
3	chr2:114516554..114518950-chr2:114645999..114648586,2	K562	blood:
4	chr2:114510034..114517579-chr2:114643441..114655407,23	MCF-7	breast:
5	chr2:114511479..114519908-chr2:114641728..114650266,13	MCF-7	breast:
6	chr2:114489220..114494215-chr2:114513189..114517576,5	K562	blood:

Variant related genes	Relation type
ENSG00000270019	Chromatin interaction
ENSG00000115091	Chromatin interaction
ENSG00000115084	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10168234	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10199704	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10200355	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10205467	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10206174	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10938	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11679707	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11682259	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11695798	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11897553	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11901060	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12711784	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13004622	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13006627	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13029093	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13034531	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13397540	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13405475	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13416930	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1349157	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1584434	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17048473	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2122095	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2305254	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2418915	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35432356	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35667749	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4849264	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4849265	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4849266	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4849269	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56213422	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56376185	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58473055	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6542171	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6704673	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6731402	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6739072	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6741521	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67850681	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7561176	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7578249	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7586800	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7587218	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7590375	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7592689	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7600550	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs935644	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9798411	0.83[AMR][1000 genomes];0.84[EUR][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	nsv1009509	chr2:114432965-114557306	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv535896	chr2:114432965-114557306	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv2883	chr2:114507889-114535199	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12711786	DDX11L2	cis	Whole Blood	GTEx
rs12711786	PS1TP4	Cis_1M	lymphoblastoid	RTeQTL
rs12711786	SLC35F5	Cis_1M	lymphoblastoid	RTeQTL
rs12711786	RPL23AP7	cis	Whole Blood	GTEx
rs12711786	SLC35F5	cis	Skin Sun Exposed Lower leg	GTEx
rs12711786	RPL23AP7	Cis_1M	lymphoblastoid	RTeQTL
rs12711786	RPL23AP7	cis	Muscle Skeletal	GTEx

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114515200-114517600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr2:114515200-114517800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr2:114515200-114517800	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr2:114515200-114517800	Weak transcription	NH-A	brain
5	chr2:114515200-114518200	Weak transcription	Psoas Muscle	Psoas
6	chr2:114515200-114519000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr2:114515200-114519600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:114515200-114519800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr2:114515200-114520400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr2:114515200-114520400	Weak transcription	Left Ventricle	heart
11	chr2:114515400-114517600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:114515400-114517600	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr2:114515400-114517600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr2:114515400-114517600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr2:114515400-114517800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:114515400-114517800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr2:114515400-114517800	Weak transcription	HSMM	muscle
18	chr2:114515400-114517800	Weak transcription	HUVEC	blood vessel
19	chr2:114515400-114517800	Weak transcription	NHLF	lung
20	chr2:114515400-114517800	Weak transcription	Osteobl	bone
21	chr2:114515400-114518000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr2:114515400-114518000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr2:114515400-114519000	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr2:114515400-114519000	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr2:114515400-114519600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr2:114515400-114519800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:114515400-114519800	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr2:114515400-114519800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr2:114515400-114519800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr2:114515400-114520000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr2:114515600-114519800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr2:114515600-114521600	Weak transcription	Duodenum Mucosa	Duodenum
33	chr2:114516200-114517200	Enhancers	HSMMtube	muscle
34	chr2:114516400-114517000	Enhancers	NHDF-Ad	bronchial
35	chr2:114516400-114517200	Enhancers	GM12878-XiMat	blood

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