Variant report

Variant	rs62020612
Chromosome Location	chr15:43818079-43818080
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:43812804..43815788-chr15:43816222..43819010,3	K562	blood:
2	chr15:43809318..43812744-chr15:43815463..43818743,6	K562	blood:
3	chr15:43806460..43809069-chr15:43815208..43818201,3	K562	blood:
4	chr15:43814200..43815983-chr15:43816527..43818249,2	MCF-7	breast:
5	chr15:43806714..43809115-chr15:43817387..43820245,2	MCF-7	breast:
6	chr15:43803434..43805458-chr15:43818001..43820886,2	K562	blood:
7	chr1:59250077..59250595-chr15:43817366..43818272,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000166963	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs12899865	0.88[EUR][1000 genomes]
rs12900259	0.85[EUR][1000 genomes]
rs12905220	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12906017	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12906481	0.89[EUR][1000 genomes]
rs12907870	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12908460	0.81[EUR][1000 genomes]
rs12910639	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12911740	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12913977	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12914122	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16957715	0.81[EUR][1000 genomes]
rs16957730	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2230451	0.81[EUR][1000 genomes]
rs34002293	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34181131	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34388946	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34633582	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34661349	0.89[EUR][1000 genomes]
rs34697113	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34860428	0.82[EUR][1000 genomes]
rs34921640	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35903301	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35958032	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs36078097	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3862138	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55801120	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs57728767	0.81[EUR][1000 genomes]
rs57938858	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60018990	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60367691	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62020574	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62020575	0.85[EUR][1000 genomes]
rs62020616	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62021180	0.81[EUR][1000 genomes]
rs66629206	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71476435	0.89[EUR][1000 genomes]
rs7173383	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7177146	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7181783	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7182292	0.89[EUR][1000 genomes]
rs72709850	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72709879	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8027748	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534649	chr15:43591116-43851142	Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	esv1846172	chr15:43632138-44116986	Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
3	esv1846701	chr15:43759774-44116986	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
4	nsv437799	chr15:43784000-43989518	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv518707	chr15:43802024-43826557	Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv832988	chr15:43804641-43976862	Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs62020612	ZSCAN29	cis	multi-tissue	Pritchard
rs62020612	LCMT2	cis	Esophagus Mucosa	GTEx
rs62020612	TGM7	cis	Esophagus Mucosa	GTEx
rs62020612	TUBGCP4	cis	Artery Tibial	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43810400-43826200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr15:43810600-43826400	Weak transcription	Spleen	Spleen
3	chr15:43810800-43824000	Weak transcription	Fetal Kidney	kidney
4	chr15:43810800-43826000	Weak transcription	Esophagus	oesophagus
5	chr15:43811000-43818600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr15:43811000-43828600	Weak transcription	Pancreas	Pancrea
7	chr15:43811200-43820600	Weak transcription	Colonic Mucosa	Colon
8	chr15:43811200-43823600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr15:43811200-43826800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr15:43811400-43829200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr15:43812000-43823200	Strong transcription	Stomach Smooth Muscle	stomach
12	chr15:43812000-43844400	Weak transcription	Fetal Brain Male	brain
13	chr15:43812200-43819000	Strong transcription	Osteobl	bone
14	chr15:43812200-43823200	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr15:43812200-43823800	Strong transcription	NHLF	lung
16	chr15:43812400-43818200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr15:43812400-43819000	ZNF genes & repeats	Fetal Stomach	stomach
18	chr15:43812400-43821400	Strong transcription	HSMMtube	muscle
19	chr15:43812400-43823200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr15:43812600-43818200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr15:43812600-43818200	Strong transcription	Left Ventricle	heart
22	chr15:43812600-43818800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr15:43812600-43819600	Strong transcription	HSMM	muscle
24	chr15:43812600-43819600	Strong transcription	NH-A	brain
25	chr15:43812600-43820000	Genic enhancers	Brain Hippocampus Middle	brain
26	chr15:43812600-43820400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr15:43812600-43823200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr15:43812600-43823200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr15:43812800-43818200	Strong transcription	Colon Smooth Muscle	Colon
30	chr15:43812800-43818800	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr15:43812800-43819800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr15:43812800-43820200	Strong transcription	NHDF-Ad	bronchial
33	chr15:43812800-43822400	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr15:43812800-43823200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr15:43812800-43823800	Strong transcription	Brain Germinal Matrix	brain
36	chr15:43812800-43824200	Strong transcription	Fetal Brain Female	brain
37	chr15:43813200-43818200	ZNF genes & repeats	Fetal Muscle Leg	muscle
38	chr15:43813200-43819200	Strong transcription	Right Ventricle	heart
39	chr15:43813600-43823400	Strong transcription	Fetal Intestine Small	intestine
40	chr15:43813800-43820000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr15:43813800-43823400	Strong transcription	Dnd41	blood
42	chr15:43814000-43818200	Strong transcription	Brain Substantia Nigra	brain
43	chr15:43814400-43826200	Weak transcription	Lung	lung
44	chr15:43814600-43826000	Weak transcription	Placenta	Placenta
45	chr15:43814800-43822000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr15:43815000-43826000	Weak transcription	Gastric	stomach
47	chr15:43815400-43818800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr15:43815400-43821800	Strong transcription	Brain Cingulate Gyrus	brain
49	chr15:43815400-43823600	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr15:43815400-43833600	Weak transcription	Placenta Amnion	Placenta Amnion

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