Variant report

Variant	rs758398
Chromosome Location	chr6:28320674-28320675
allele	C/T
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28225627..28229530-chr6:28318492..28321477,3	K562	blood:
2	chr6:28228030..28230750-chr6:28318492..28321168,2	K562	blood:
3	chr6:28183629..28195178-chr6:28316250..28325659,29	K562	blood:
4	chr6:28192912..28194626-chr6:28318304..28321178,2	MCF-7	breast:
5	chr6:28217257..28219975-chr6:28319678..28321725,2	K562	blood:
6	chr6:28318727..28321441-chr6:28336675..28338219,2	K562	blood:
7	chr6:28300850..28305636-chr6:28315212..28320749,12	MCF-7	breast:
8	chr6:28182735..28195387-chr6:28315960..28325841,32	K562	blood:
9	chr6:28101857..28106060-chr6:28315199..28321034,6	K562	blood:
10	chr6:27857264..27863272-chr6:28318615..28325449,9	K562	blood:
11	chr6:28085276..28086790-chr6:28319543..28321327,2	K562	blood:
12	chr6:28233021..28237962-chr6:28316234..28324041,9	K562	blood:

No data

Variant related genes	Relation type
ENSG00000196331	Chromatin interaction
ENSG00000269293	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000137185	Chromatin interaction
ENSG00000187626	Chromatin interaction
ENSG00000197062	Chromatin interaction
ENSG00000189134	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000261839	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000176933	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12000	0.80[CHB][hapmap]
rs12180820	0.86[CHB][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1233710	0.90[JPT][hapmap]
rs1361386	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1416920	0.86[CHB][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1635	0.95[JPT][hapmap]
rs1997660	0.83[EUR][1000 genomes]
rs2108926	0.86[CHB][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3800327	0.82[JPT][hapmap]
rs4713158	0.83[EUR][1000 genomes]
rs6456815	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6936644	0.83[ASN][1000 genomes]
rs6942030	0.86[CHB][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs707907	0.83[EUR][1000 genomes]
rs7750106	0.95[JPT][hapmap]
rs7772827	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs853683	0.83[EUR][1000 genomes]
rs853690	0.83[EUR][1000 genomes]
rs853693	0.83[EUR][1000 genomes]
rs9468333	0.83[EUR][1000 genomes]
rs9468334	0.80[ASN][1000 genomes]
rs9468344	0.86[CHB][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs758398	ZSCAN23	cis	Artery Tibial	GTEx
rs758398	AL022393.7	cis	Heart Left Ventricle	GTEx
rs758398	AL022393.7	cis	Nerve Tibial	GTEx
rs758398	RP5-874C20.3	cis	Thyroid	GTEx
rs758398	AL022393.7	cis	Esophagus Muscularis	GTEx
rs758398	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs758398	AL022393.7	cis	Muscle Skeletal	GTEx
rs758398	ZSCAN31	cis	lung	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28317200-28322000	Active TSS	Rectal Smooth Muscle	rectum
2	chr6:28317200-28322200	Active TSS	Stomach Smooth Muscle	stomach
3	chr6:28318200-28321800	Weak transcription	Spleen	Spleen
4	chr6:28318200-28322800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:28318400-28320800	Weak transcription	Esophagus	oesophagus
6	chr6:28318400-28321600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:28318400-28321600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:28318400-28321800	Weak transcription	Gastric	stomach
9	chr6:28318400-28322200	Weak transcription	Placenta	Placenta
10	chr6:28318400-28323000	Weak transcription	Fetal Muscle Trunk	muscle
11	chr6:28318400-28323600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr6:28318400-28332000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:28318400-28350800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr6:28318600-28322800	Weak transcription	NHDF-Ad	bronchial
15	chr6:28318600-28323000	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr6:28318800-28322200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr6:28318800-28322800	Weak transcription	Fetal Kidney	kidney
18	chr6:28319000-28321200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr6:28319000-28321600	Weak transcription	Osteobl	bone
20	chr6:28319000-28323000	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr6:28319000-28323200	Weak transcription	Primary B cells from peripheral blood	blood
22	chr6:28319000-28323200	Weak transcription	Small Intestine	intestine
23	chr6:28319200-28321000	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr6:28319200-28321000	Weak transcription	Brain Cingulate Gyrus	brain
25	chr6:28319200-28321000	Weak transcription	Left Ventricle	heart
26	chr6:28319200-28321200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr6:28319200-28321200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:28319200-28321200	Weak transcription	Brain Hippocampus Middle	brain
29	chr6:28319200-28321200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr6:28319200-28321400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:28319200-28321400	Weak transcription	Fetal Muscle Leg	muscle
32	chr6:28319200-28321400	Weak transcription	Psoas Muscle	Psoas
33	chr6:28319200-28321600	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr6:28319200-28321600	Weak transcription	Fetal Stomach	stomach
35	chr6:28319200-28321800	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr6:28319200-28322000	Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr6:28319200-28322200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr6:28319200-28322200	Weak transcription	Lung	lung
39	chr6:28319200-28322200	Weak transcription	A549	lung
40	chr6:28319200-28322200	Weak transcription	HMEC	breast
41	chr6:28319200-28322400	Weak transcription	Duodenum Mucosa	Duodenum
42	chr6:28319200-28322800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr6:28319200-28322800	Weak transcription	Right Ventricle	heart
44	chr6:28319200-28323000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr6:28319200-28323000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr6:28319200-28323000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr6:28319200-28323000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr6:28319200-28323000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr6:28319200-28323000	Weak transcription	Fetal Intestine Large	intestine
50	chr6:28319200-28323200	Weak transcription	H1 Cell Line	embryonic stem cell

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