Variant report

Variant	rs1005125
Chromosome Location	chr6:28367355-28367356
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28366385..28368709-chr6:28493666..28495776,2	K562	blood:
2	chr6:28315597..28319153-chr6:28366055..28369015,3	K562	blood:
3	chr6:28364231..28371937-chr6:28372195..28378158,17	K562	blood:
4	chr6:28366682..28368772-chr6:28423873..28426480,2	K562	blood:
5	chr6:28082452..28085124-chr6:28366168..28368167,2	K562	blood:
6	chr6:28302165..28304933-chr6:28366158..28368845,2	K562	blood:
7	chr11:10829981..10830691-chr6:28367328..28367828,2	Hela-S3	cervix:
8	chr6:28191542..28193155-chr6:28365970..28368318,2	K562	blood:
9	chr6:28225119..28227553-chr6:28366156..28368716,2	K562	blood:
10	chr6:28366328..28368330-chr6:28583082..28585639,2	K562	blood:
11	chr6:28366328..28369247-chr6:28582607..28584582,2	K562	blood:
12	chr6:27857864..27860590-chr6:28365932..28368425,2	K562	blood:
13	chr6:28191542..28194803-chr6:28365970..28368645,4	K562	blood:
14	chr6:28109524..28111212-chr6:28366058..28368601,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000235109	Chromatin interaction
ENSG00000189298	Chromatin interaction
ENSG00000198315	Chromatin interaction
ENSG00000137185	Chromatin interaction
ENSG00000187626	Chromatin interaction
ENSG00000219392	Chromatin interaction
ENSG00000110321	Chromatin interaction
ENSG00000189134	Chromatin interaction
ENSG00000219262	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000224586	Chromatin interaction
ENSG00000251877	Chromatin interaction
ENSG00000232040	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1052215	0.95[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10946954	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1124132	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1150694	1.00[YRI][hapmap]
rs1150705	0.81[EUR][1000 genomes]
rs1150707	0.87[CEU][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs1150709	0.87[CEU][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs1150716	0.84[EUR][1000 genomes]
rs1150718	1.00[YRI][hapmap]
rs1150721	1.00[YRI][hapmap]
rs1150724	1.00[YRI][hapmap]
rs1150726	1.00[YRI][hapmap]
rs12214383	1.00[YRI][hapmap]
rs1233713	0.87[CEU][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs13408	1.00[YRI][hapmap]
rs1361387	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1531681	1.00[YRI][hapmap]
rs1736891	0.87[CEU][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs1736895	1.00[YRI][hapmap]
rs1997660	1.00[YRI][hapmap]
rs2023493	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2108927	0.81[EUR][1000 genomes]
rs213232	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs213236	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs213237	0.95[CEU][hapmap];0.89[CHB][hapmap];0.81[JPT][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs213238	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs213240	0.90[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2142730	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs2247002	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2394049	1.00[YRI][hapmap]
rs2531803	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2531805	0.82[AMR][1000 genomes]
rs2531806	0.86[AMR][1000 genomes]
rs2531825	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2531831	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2531832	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2859348	0.86[CEU][hapmap];0.90[AMR][1000 genomes]
rs2859365	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4455662	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs707907	1.00[YRI][hapmap]
rs7206	0.87[CEU][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs728122	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs853683	1.00[YRI][hapmap]
rs853684	0.87[CEU][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs853690	1.00[YRI][hapmap]
rs853693	1.00[YRI][hapmap]
rs916403	0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9301	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs9368565	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9468333	1.00[YRI][hapmap]
rs9468372	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]

mRNA abundance (count:22)

SNP	Gene	Cis/trans	Tissue	Source
rs1005125	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs1005125	RP5-874C20.3	cis	Esophagus Muscularis	GTEx
rs1005125	ZSCAN23	cis	Muscle Skeletal	GTEx
rs1005125	AL022393.7	cis	Heart Left Ventricle	GTEx
rs1005125	AL022393.7	cis	Artery Aorta	GTEx
rs1005125	ZNF323	cis	Frontal Cortex	GTEx
rs1005125	ZSCAN31	cis	Esophagus Muscularis	GTEx
rs1005125	ZSCAN23	cis	Artery Tibial	GTEx
rs1005125	ZSCAN23	cis	Adipose Subcutaneous	GTEx
rs1005125	AL022393.7	cis	lung	GTEx
rs1005125	ZSCAN31	cis	Muscle Skeletal	GTEx
rs1005125	RP5-874C20.3	cis	Nerve Tibial	GTEx
rs1005125	AL022393.7	cis	Nerve Tibial	GTEx
rs1005125	AL022393.7	cis	Muscle Skeletal	GTEx
rs1005125	ZSCAN23	cis	lung	GTEx
rs1005125	ZSCAN31	cis	lung	GTEx
rs1005125	AL022393.7	cis	Esophagus Muscularis	GTEx
rs1005125	ZSCAN31	cis	Stomach	GTEx
rs1005125	ZSCAN31	cis	Thyroid	GTEx
rs1005125	AL022393.7	cis	Artery Tibial	GTEx
rs1005125	RP5-874C20.3	cis	Thyroid	GTEx
rs1005125	TRIM27	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28366000-28368000	Active TSS	HSMMtube	muscle
2	chr6:28366000-28368200	Active TSS	H1 Cell Line	embryonic stem cell
3	chr6:28366000-28368200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr6:28366000-28368200	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr6:28366000-28368200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr6:28366200-28367800	Active TSS	Muscle Satellite Cultured Cells	--
7	chr6:28366200-28367800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:28366200-28368000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr6:28366200-28368000	Active TSS	H9 Cell Line	embryonic stem cell
10	chr6:28366200-28368000	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr6:28366200-28368000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr6:28366200-28368000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:28366200-28368000	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr6:28366200-28368000	Active TSS	Placenta Amnion	Placenta Amnion
15	chr6:28366200-28368200	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr6:28366200-28368200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr6:28366200-28368200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr6:28366200-28368200	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr6:28366200-28368200	Active TSS	iPS-18 Cell Line	embryonic stem cell
20	chr6:28366200-28368200	Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr6:28366200-28368200	Active TSS	Primary hematopoietic stem cells short term culture	blood
22	chr6:28366200-28368200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr6:28366200-28368200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
24	chr6:28366200-28368200	Active TSS	Fetal Intestine Small	intestine
25	chr6:28366200-28368200	Active TSS	Rectal Mucosa Donor 29	rectum
26	chr6:28366200-28368200	Active TSS	Stomach Smooth Muscle	stomach
27	chr6:28366200-28368200	Active TSS	K562	blood
28	chr6:28366200-28368400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr6:28366200-28368400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr6:28366200-28368400	Active TSS	Brain Anterior Caudate	brain
31	chr6:28366200-28368400	Active TSS	Brain Inferior Temporal Lobe	brain
32	chr6:28366200-28368400	Active TSS	Osteobl	bone
33	chr6:28366400-28367600	Active TSS	Cortex derived primary cultured neurospheres	brain
34	chr6:28366400-28367600	Active TSS	NHEK	skin
35	chr6:28366400-28367800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr6:28366400-28367800	Active TSS	GM12878-XiMat	blood
37	chr6:28366400-28367800	Active TSS	Hela-S3	cervix
38	chr6:28366400-28367800	Active TSS	HMEC	breast
39	chr6:28366400-28368000	Active TSS	HUES48 Cell Line	embryonic stem cell
40	chr6:28366400-28368000	Active TSS	Colon Smooth Muscle	Colon
41	chr6:28366400-28368200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr6:28366400-28368200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr6:28366400-28368200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr6:28366400-28368200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr6:28366400-28368200	Active TSS	Brain Hippocampus Middle	brain
46	chr6:28366400-28368400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr6:28366400-28368400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr6:28366400-28368400	Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr6:28366400-28368400	Active TSS	Fetal Brain Female	brain
50	chr6:28366400-28368400	Active TSS	NHDF-Ad	bronchial

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