Variant report

Variant	rs1512662
Chromosome Location	chr3:110246388-110246389
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	chr3:110245688..110247478-chr3:110251852..110254191,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-553A10.1.1-2	chr3:110246329-110246613	XLOC_003212

Extended variants
information (count: 100 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10934056	0.82[EUR][1000 genomes]
rs10934063	0.84[EUR][1000 genomes]
rs10934064	0.84[EUR][1000 genomes]
rs11719761	0.89[ASN][1000 genomes]
rs11923659	0.84[ASN][1000 genomes]
rs11925026	0.84[EUR][1000 genomes]
rs12053901	0.84[EUR][1000 genomes]
rs12054102	0.81[AMR][1000 genomes]
rs12493010	0.82[EUR][1000 genomes]
rs13078633	0.84[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1462295	0.84[EUR][1000 genomes]
rs1606350	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16856946	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17202417	0.89[ASN][1000 genomes]
rs1913090	0.82[EUR][1000 genomes]
rs2055968	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2895375	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4682179	0.89[ASN][1000 genomes]
rs57198450	0.89[EUR][1000 genomes]
rs57680282	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58500543	0.84[EUR][1000 genomes]
rs59612531	0.89[EUR][1000 genomes]
rs59985710	0.95[EUR][1000 genomes]
rs60302938	0.84[EUR][1000 genomes]
rs62270060	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62270063	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62270076	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62270083	0.95[EUR][1000 genomes]
rs62270086	0.95[EUR][1000 genomes]
rs62270095	0.95[EUR][1000 genomes]
rs62270100	0.95[EUR][1000 genomes]
rs62270121	0.84[EUR][1000 genomes]
rs62270122	0.84[EUR][1000 genomes]
rs62270123	0.84[EUR][1000 genomes]
rs62270124	0.89[EUR][1000 genomes]
rs62270127	0.84[EUR][1000 genomes]
rs62270128	0.89[EUR][1000 genomes]
rs62270130	0.84[EUR][1000 genomes]
rs62270134	0.89[EUR][1000 genomes]
rs62271562	0.81[AMR][1000 genomes]
rs62271576	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62271586	0.84[EUR][1000 genomes]
rs62271587	0.84[EUR][1000 genomes]
rs62271588	0.84[EUR][1000 genomes]
rs62271591	0.84[EUR][1000 genomes]
rs62271592	0.84[EUR][1000 genomes]
rs62271606	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62271607	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62271608	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62271609	0.95[EUR][1000 genomes]
rs62271610	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62271612	0.95[EUR][1000 genomes]
rs62271615	0.95[EUR][1000 genomes]
rs62271616	0.95[EUR][1000 genomes]
rs62271618	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62271620	0.95[EUR][1000 genomes]
rs62271621	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62271636	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62271639	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62271642	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62271644	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62271646	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62271647	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62271763	0.84[EUR][1000 genomes]
rs62271766	0.89[EUR][1000 genomes]
rs62271784	0.89[EUR][1000 genomes]
rs6765569	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6768474	0.86[EUR][1000 genomes]
rs6772035	0.84[EUR][1000 genomes]
rs6776067	0.84[EUR][1000 genomes]
rs6781483	0.95[EUR][1000 genomes]
rs6784648	0.84[EUR][1000 genomes]
rs7617903	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7626514	0.86[ASN][1000 genomes]
rs7628733	0.84[EUR][1000 genomes]
rs7630242	0.86[ASN][1000 genomes]
rs7631316	0.95[EUR][1000 genomes]
rs7632974	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7634524	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7650722	0.84[EUR][1000 genomes]
rs7652062	0.86[EUR][1000 genomes]
rs9653909	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9809312	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9809608	0.86[ASN][1000 genomes]
rs9825259	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs9858359	0.84[EUR][1000 genomes]
rs986205	0.82[EUR][1000 genomes]
rs986206	0.82[EUR][1000 genomes]
rs9873714	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999414	chr3:110103126-110340180	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv829670	chr3:110134650-110308256	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv520365	chr3:110155172-110441165	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1001144	chr3:110158316-110431113	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv536687	chr3:110158316-110431113	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1001810	chr3:110158316-110522247	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1010230	chr3:110204439-110588814	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv536688	chr3:110204439-110588814	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv829672	chr3:110206693-110361632	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1011034	chr3:110209344-110559021	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv536689	chr3:110209344-110559021	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:110244800-110246800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:110244800-110248200	Enhancers	HUVEC	blood vessel
3	chr3:110245200-110247000	Enhancers	Hela-S3	cervix
4	chr3:110245200-110247000	Enhancers	HMEC	breast
5	chr3:110245200-110247200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr3:110245200-110247200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:110245200-110247800	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr3:110245200-110248000	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr3:110245400-110246600	Enhancers	HSMMtube	muscle
10	chr3:110245400-110246800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:110245400-110247000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:110245400-110247000	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr3:110245400-110247000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr3:110245400-110247200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:110245400-110247600	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr3:110245400-110247600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:110245400-110247800	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr3:110245400-110248200	Enhancers	Osteobl	bone
19	chr3:110245600-110246600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:110245600-110247800	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr3:110245800-110246600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr3:110245800-110246600	Flanking Active TSS	HSMM	muscle
23	chr3:110245800-110246800	Enhancers	K562	blood
24	chr3:110245800-110248200	Enhancers	Placenta Amnion	Placenta Amnion
25	chr3:110246000-110246400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr3:110246000-110247400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:110246200-110246400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
28	chr3:110246200-110246400	Enhancers	Muscle Satellite Cultured Cells	--
29	chr3:110246200-110246400	Enhancers	A549	lung
30	chr3:110246200-110246400	Enhancers	NHDF-Ad	bronchial
31	chr3:110246200-110246600	Flanking Active TSS	NHEK	skin
32	chr3:110246200-110246600	Enhancers	NHLF	lung
33	chr3:110246200-110246800	Enhancers	Fetal Intestine Small	intestine
34	chr3:110246200-110247000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr3:110246200-110247200	Enhancers	NH-A	brain
36	chr3:110246200-110247400	Enhancers	Fetal Intestine Large	intestine

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