Variant report

Variant	rs9368565
Chromosome Location	chr6:28345210-28345211
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28320843..28322406-chr6:28343644..28345463,2	MCF-7	breast:
2	chr6:28336184..28339998-chr6:28343727..28348047,5	K562	blood:
3	chr6:28340056..28341598-chr6:28344823..28347301,2	K562	blood:
4	chr6:28336184..28339617-chr6:28343727..28347086,4	K562	blood:

Variant related genes	Relation type
ENSG00000235109	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1005125	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1052215	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10946954	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1124132	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1150705	0.82[EUR][1000 genomes]
rs1150707	0.82[EUR][1000 genomes]
rs1150709	0.82[EUR][1000 genomes]
rs1150716	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1233713	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1736891	0.81[EUR][1000 genomes]
rs2023493	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2108927	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs213232	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs213236	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs213237	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs213238	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs213240	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2142730	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2191035	0.80[ASN][1000 genomes]
rs2247002	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2531805	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2531806	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2531825	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2531831	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2531832	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2859348	0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2859365	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4455662	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7206	0.82[EUR][1000 genomes]
rs728122	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs853684	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9301	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9468372	0.85[EUR][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	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:21)

SNP	Gene	Cis/trans	Tissue	Source
rs9368565	ZSCAN31	cis	Stomach	GTEx
rs9368565	RP5-874C20.3	cis	Thyroid	GTEx
rs9368565	TRIM27	cis	Skin Sun Exposed Lower leg	GTEx
rs9368565	ZSCAN31	cis	Esophagus Muscularis	GTEx
rs9368565	AL022393.7	cis	Muscle Skeletal	GTEx
rs9368565	ZSCAN23	cis	lung	GTEx
rs9368565	AL022393.7	cis	Artery Tibial	GTEx
rs9368565	ZSCAN23	cis	Artery Tibial	GTEx
rs9368565	AL022393.7	cis	Heart Left Ventricle	GTEx
rs9368565	AL022393.7	cis	Esophagus Muscularis	GTEx
rs9368565	ZSCAN31	cis	Thyroid	GTEx
rs9368565	RP5-874C20.3	cis	Nerve Tibial	GTEx
rs9368565	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs9368565	AL022393.7	cis	lung	GTEx
rs9368565	AL022393.7	cis	Artery Aorta	GTEx
rs9368565	ZSCAN31	cis	lung	GTEx
rs9368565	RP5-874C20.3	cis	Esophagus Muscularis	GTEx
rs9368565	ZSCAN23	cis	Adipose Subcutaneous	GTEx
rs9368565	ZSCAN31	cis	Muscle Skeletal	GTEx
rs9368565	AL022393.7	cis	Nerve Tibial	GTEx
rs9368565	ZSCAN23	cis	Muscle Skeletal	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28318400-28350800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:28324400-28347600	Weak transcription	NHDF-Ad	bronchial
3	chr6:28324400-28347800	Weak transcription	Fetal Brain Male	brain
4	chr6:28324400-28348200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr6:28324400-28357200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr6:28324400-28357600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr6:28324600-28349400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr6:28324600-28349600	Weak transcription	NHEK	skin
9	chr6:28324600-28358600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr6:28325400-28350800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr6:28332000-28350600	Weak transcription	Psoas Muscle	Psoas
12	chr6:28333800-28345800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:28333800-28347800	Weak transcription	HUVEC	blood vessel
14	chr6:28333800-28348000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr6:28333800-28349800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr6:28333800-28349800	Weak transcription	Pancreas	Pancrea
17	chr6:28333800-28350800	Weak transcription	Lung	lung
18	chr6:28333800-28351000	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr6:28334000-28345600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:28334000-28346600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:28334000-28346800	Weak transcription	Fetal Kidney	kidney
22	chr6:28334000-28348000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr6:28334000-28350000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr6:28334000-28350600	Weak transcription	Colonic Mucosa	Colon
25	chr6:28334000-28350800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr6:28334200-28345600	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr6:28334200-28345600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr6:28334200-28346000	Weak transcription	Fetal Intestine Small	intestine
29	chr6:28334200-28346000	Weak transcription	HMEC	breast
30	chr6:28334200-28346200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:28334200-28347800	Weak transcription	NHLF	lung
32	chr6:28334200-28348000	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr6:28334200-28348000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr6:28334200-28348200	Weak transcription	Brain Substantia Nigra	brain
35	chr6:28334200-28348800	Weak transcription	Fetal Heart	heart
36	chr6:28334200-28349400	Weak transcription	Right Ventricle	heart
37	chr6:28334200-28349800	Weak transcription	Aorta	Aorta
38	chr6:28334200-28351000	Weak transcription	Gastric	stomach
39	chr6:28334200-28351200	Weak transcription	Spleen	Spleen
40	chr6:28334400-28345600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr6:28334400-28345600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr6:28334400-28345600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr6:28334400-28345600	Weak transcription	Fetal Intestine Large	intestine
44	chr6:28334400-28345800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr6:28334400-28345800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr6:28334400-28347200	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr6:28334400-28347400	Weak transcription	HSMM	muscle
48	chr6:28334400-28347600	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr6:28334400-28347800	Weak transcription	Brain Angular Gyrus	brain
50	chr6:28334400-28347800	Weak transcription	Brain Hippocampus Middle	brain

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