Variant report

Variant	rs3129063
Chromosome Location	chr6:29645613-29645614
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 28 )

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

rs_ID	r²[population]
rs2107203	0.81[ASN][1000 genomes]
rs2158290	0.81[ASN][1000 genomes]
rs2535238	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2535274	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2535275	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2747421	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2747427	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2747428	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2747429	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2747457	0.81[ASN][1000 genomes]
rs2747460	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2907897	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs29218	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs29228	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3094579	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3094724	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3094725	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3094730	0.82[ASN][1000 genomes]
rs3094731	0.82[ASN][1000 genomes]
rs3094732	0.81[ASN][1000 genomes]
rs3095266	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3095269	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3095271	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3095284	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3095290	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3095294	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3116802	0.81[ASN][1000 genomes]
rs3116803	0.81[ASN][1000 genomes]
rs3116811	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3116814	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3117289	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3117295	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3117299	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3117301	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3117312	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3117318	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3129033	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3129035	0.85[ASN][1000 genomes]
rs3129036	0.83[EUR][1000 genomes]
rs3129039	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3129046	0.82[ASN][1000 genomes]
rs3129047	0.81[ASN][1000 genomes]
rs3129048	0.81[ASN][1000 genomes]
rs3129055	0.81[ASN][1000 genomes]
rs3129056	0.81[ASN][1000 genomes]
rs3129058	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129061	0.81[ASN][1000 genomes]
rs3129062	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3129065	0.81[ASN][1000 genomes]
rs3129066	0.81[ASN][1000 genomes]
rs3129067	0.82[ASN][1000 genomes]
rs3129069	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3129070	0.81[ASN][1000 genomes]
rs3129072	0.81[ASN][1000 genomes]
rs3129073	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3129084	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3129086	0.81[ASN][1000 genomes]
rs3129092	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3129189	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3130251	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3131864	0.81[ASN][1000 genomes]
rs3131865	0.81[ASN][1000 genomes]
rs3131866	0.81[ASN][1000 genomes]
rs3131867	0.82[ASN][1000 genomes]
rs3131868	0.81[ASN][1000 genomes]
rs3131870	0.81[ASN][1000 genomes]
rs3131871	0.81[ASN][1000 genomes]
rs3131872	0.81[ASN][1000 genomes]
rs3131873	0.81[ASN][1000 genomes]
rs3131874	0.81[ASN][1000 genomes]
rs3131889	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3131890	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3131895	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3131898	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs374317	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs375248	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs375984	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs376319	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs387640	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs387642	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs417764	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs448380	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs448489	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9258017	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9258048	0.81[ASN][1000 genomes]
rs9258068	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9258074	0.81[ASN][1000 genomes]
rs9258079	0.81[ASN][1000 genomes]
rs9258083	0.81[ASN][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	esv2758039	chr6:29469101-29672665	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv2759411	chr6:29469101-29672665	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv883530	chr6:29645038-29677641	Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:28)

SNP	Gene	Cis/trans	Tissue	Source
rs3129063	ZFP57	cis	Heart Left Ventricle	GTEx
rs3129063	HLA-A	trans	brain	seeQTL
rs3129063	KIT	trans	multi-tissue	Pritchard
rs3129063	ZFP57	cis	Artery Aorta	GTEx
rs3129063	BTN3A2	cis	multi-tissue	Pritchard
rs3129063	HIST1H2BM	cis	cerebellum	SCAN
rs3129063	ZFP57	cis	Whole Blood	GTEx
rs3129063	HLA-F-AS1	cis	Whole Blood	GTEx
rs3129063	HLA-A	cis	multi-tissue	Pritchard
rs3129063	ZFP57	cis	Thyroid	GTEx
rs3129063	HLA-K	cis	Whole Blood	GTEx
rs3129063	ZFP57	cis	Esophagus Muscularis	GTEx
rs3129063	HLA-A	cis	brain	seeQTL
rs3129063	BTN3A3	cis	parietal	SCAN
rs3129063	ZFP57	cis	Artery Tibial	GTEx
rs3129063	ZFP57	cis	Stomach	GTEx
rs3129063	ZFP57	cis	Esophagus Mucosa	GTEx
rs3129063	ZFP57	cis	Nerve Tibial	GTEx
rs3129063	HLA-G	cis	multi-tissue	Pritchard
rs3129063	ZFP57	cis	multi-tissue	Pritchard
rs3129063	ZFP57	cis	lymphoblastoid	seeQTL
rs3129063	ZKSCAN3	cis	parietal	SCAN
rs3129063	ZNF323	cis	parietal	SCAN
rs3129063	ZFP57	cis	lung	GTEx
rs3129063	ZFP57	cis	Adipose Subcutaneous	GTEx
rs3129063	HLA-H	cis	multi-tissue	Pritchard
rs3129063	HIST1H3I	cis	cerebellum	SCAN
rs3129063	ZFP57	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29625000-29663600	Weak transcription	Right Atrium	heart
2	chr6:29639600-29647400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr6:29643000-29646400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:29643000-29648800	Enhancers	HMEC	breast
5	chr6:29643200-29648400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:29643400-29648400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:29643800-29647600	Enhancers	Fetal Heart	heart
8	chr6:29644400-29646200	Enhancers	H9 Cell Line	embryonic stem cell
9	chr6:29644600-29645800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr6:29644600-29646000	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr6:29644600-29647800	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr6:29644800-29646200	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr6:29644800-29647400	Enhancers	Hela-S3	cervix
14	chr6:29644800-29647600	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr6:29644800-29648000	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr6:29644800-29648000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr6:29645000-29646800	Enhancers	H1 Cell Line	embryonic stem cell
18	chr6:29645000-29648000	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr6:29645200-29646200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr6:29645200-29648200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr6:29645200-29648400	Weak transcription	Primary hematopoietic stem cells	blood
22	chr6:29645400-29645800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr6:29645400-29646000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr6:29645400-29646000	Enhancers	NHEK	skin
25	chr6:29645400-29646600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr6:29645600-29647000	Weak transcription	HUES48 Cell Line	embryonic stem cell

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