Variant report

Variant	rs4713158
Chromosome Location	chr6:28277771-28277772
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:28224904..28226983-chr6:28276563..28279040,2	K562	blood:
2	chr6:28277054..28279277-chr6:28294657..28297286,2	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1150670	0.83[AMR][1000 genomes]
rs1150679	0.83[AMR][1000 genomes]
rs1150686	0.83[AMR][1000 genomes]
rs1150690	0.81[AMR][1000 genomes]
rs1150705	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1150707	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1150709	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1150711	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1150716	0.93[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1150718	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1150721	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1150724	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1150726	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12180820	0.85[EUR][1000 genomes]
rs12214383	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1225618	0.82[AMR][1000 genomes]
rs1225710	0.83[AMR][1000 genomes]
rs1225715	0.82[AMR][1000 genomes]
rs1233660	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1233713	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13408	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1361386	0.85[EUR][1000 genomes]
rs1416920	0.86[EUR][1000 genomes]
rs1531681	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1736891	0.88[AMR][1000 genomes]
rs1736895	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1778484	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1997660	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2021826	0.83[AMR][1000 genomes]
rs2108926	0.86[EUR][1000 genomes]
rs213238	0.83[ASN][1000 genomes]
rs213240	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2142730	0.93[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2394049	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2622322	0.82[AMR][1000 genomes]
rs2791333	0.83[AMR][1000 genomes]
rs6456815	0.85[EUR][1000 genomes]
rs6942030	0.85[EUR][1000 genomes]
rs707907	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7206	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs758398	0.83[EUR][1000 genomes]
rs7772827	0.84[EUR][1000 genomes]
rs853683	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs853684	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs853690	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs853693	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9301	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9468333	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468344	0.86[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:16)

SNP	Gene	Cis/trans	Tissue	Source
rs4713158	ZSCAN23	cis	Adipose Subcutaneous	GTEx
rs4713158	AL022393.7	cis	Nerve Tibial	GTEx
rs4713158	ZKSCAN3	cis	Skin Sun Exposed Lower leg	GTEx
rs4713158	ZSCAN23	cis	Artery Tibial	GTEx
rs4713158	AL022393.7	cis	Muscle Skeletal	GTEx
rs4713158	ZSCAN31	cis	Stomach	GTEx
rs4713158	ZSCAN31	cis	lung	GTEx
rs4713158	AL022393.7	cis	Heart Left Ventricle	GTEx
rs4713158	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs4713158	ZSCAN23	cis	Muscle Skeletal	GTEx
rs4713158	RP5-874C20.3	cis	Thyroid	GTEx
rs4713158	AL022393.7	cis	Esophagus Muscularis	GTEx
rs4713158	ZSCAN31	cis	Thyroid	GTEx
rs4713158	RP5-874C20.3	cis	Nerve Tibial	GTEx
rs4713158	RP5-874C20.3	cis	Esophagus Muscularis	GTEx
rs4713158	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28250000-28293800	Weak transcription	Gastric	stomach
2	chr6:28250400-28278600	Weak transcription	Duodenum Mucosa	Duodenum
3	chr6:28250600-28280600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr6:28251000-28278800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:28255200-28278600	Weak transcription	Esophagus	oesophagus
6	chr6:28255200-28278600	Weak transcription	Pancreas	Pancrea
7	chr6:28255200-28278800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:28255200-28283000	Weak transcription	HSMMtube	muscle
9	chr6:28255200-28293800	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr6:28255400-28278400	Weak transcription	HepG2	liver
11	chr6:28256400-28277800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr6:28256600-28280800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:28257600-28278800	Weak transcription	NHDF-Ad	bronchial
14	chr6:28257800-28279000	Weak transcription	HMEC	breast
15	chr6:28264800-28278600	Weak transcription	Fetal Intestine Small	intestine
16	chr6:28265000-28280600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr6:28265400-28278800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr6:28266400-28278800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr6:28268400-28280600	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr6:28268800-28293400	Weak transcription	Colon Smooth Muscle	Colon
21	chr6:28269200-28278600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr6:28269200-28291600	Weak transcription	Right Ventricle	heart
23	chr6:28269400-28278600	Weak transcription	Fetal Intestine Large	intestine
24	chr6:28269400-28280800	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr6:28269800-28280000	Weak transcription	Left Ventricle	heart
26	chr6:28270000-28279000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr6:28270000-28280800	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr6:28270000-28290400	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr6:28270000-28291400	Weak transcription	Ovary	ovary
30	chr6:28270000-28291600	Weak transcription	Brain Anterior Caudate	brain
31	chr6:28270000-28291600	Weak transcription	Fetal Brain Female	brain
32	chr6:28270000-28293400	Weak transcription	Brain Angular Gyrus	brain
33	chr6:28270400-28279600	Weak transcription	Stomach Smooth Muscle	stomach
34	chr6:28271200-28293800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr6:28271400-28293400	Weak transcription	Brain Cingulate Gyrus	brain
36	chr6:28272400-28279200	Weak transcription	K562	blood
37	chr6:28272400-28291800	Weak transcription	Brain Hippocampus Middle	brain
38	chr6:28272400-28293200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr6:28272600-28292000	Weak transcription	Fetal Muscle Leg	muscle
40	chr6:28272600-28292600	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr6:28272600-28292600	Weak transcription	Brain Germinal Matrix	brain
42	chr6:28273000-28291600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr6:28276800-28279400	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr6:28277000-28279400	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr6:28277200-28277800	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr6:28277200-28279000	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr6:28277600-28278000	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr6:28277600-28278400	Enhancers	ES-WA7 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links