Variant report

Variant	rs7750526
Chromosome Location	chr6:28336004-28336005
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28326753..28329477-chr6:28335475..28338195,2	K562	blood:
2	chr6:28333760..28336072-chr6:28337561..28339337,2	K562	blood:
3	chr6:28335113..28339342-chr6:28340295..28342925,4	K562	blood:
4	chr6:28335113..28339342-chr6:28340295..28342683,4	K562	blood:
5	chr6:28303740..28306465-chr6:28335906..28338559,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235109	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1005126	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11751928	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs13190937	0.84[ASN][1000 genomes]
rs13193272	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13196606	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13199081	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13203055	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13209596	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13217326	0.89[EUR][1000 genomes]
rs16894091	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16894106	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2232427	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28505234	0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs3799499	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3799500	0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs57071502	0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs58020991	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6902687	0.84[ASN][1000 genomes]
rs6905380	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6931359	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6940744	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71559081	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7740429	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7754960	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7774981	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9468356	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9468358	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9468364	0.82[ASN][1000 genomes]
rs9969098	0.97[EUR][1000 genomes];0.84[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7750526	AL022393.7	cis	Heart Left Ventricle	GTEx
rs7750526	ZSCAN23	cis	Artery Tibial	GTEx
rs7750526	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs7750526	RP5-874C20.3	cis	Esophagus Muscularis	GTEx
rs7750526	AL022393.7	cis	Muscle Skeletal	GTEx
rs7750526	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs7750526	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL

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	chr6:28324800-28341600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr6:28325400-28350800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr6:28326800-28336200	Strong transcription	Adipose Nuclei	Adipose
13	chr6:28327000-28336200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr6:28327000-28336200	Strong transcription	Fetal Stomach	stomach
15	chr6:28327000-28337600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr6:28327200-28338400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr6:28328000-28337000	Strong transcription	Liver	Liver
18	chr6:28328200-28336800	Strong transcription	Fetal Muscle Leg	muscle
19	chr6:28330800-28337600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr6:28330800-28338600	Strong transcription	Primary T cells from cord blood	blood
21	chr6:28331200-28336600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr6:28331200-28337600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr6:28332000-28350600	Weak transcription	Psoas Muscle	Psoas
24	chr6:28333800-28345800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:28333800-28347800	Weak transcription	HUVEC	blood vessel
26	chr6:28333800-28348000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr6:28333800-28349800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr6:28333800-28349800	Weak transcription	Pancreas	Pancrea
29	chr6:28333800-28350800	Weak transcription	Lung	lung
30	chr6:28333800-28351000	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr6:28334000-28338200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr6:28334000-28338400	Weak transcription	Fetal Brain Female	brain
33	chr6:28334000-28345600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr6:28334000-28346600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr6:28334000-28346800	Weak transcription	Fetal Kidney	kidney
36	chr6:28334000-28348000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr6:28334000-28350000	Weak transcription	Rectal Smooth Muscle	rectum
38	chr6:28334000-28350600	Weak transcription	Colonic Mucosa	Colon
39	chr6:28334000-28350800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr6:28334200-28336400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr6:28334200-28345200	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr6:28334200-28345600	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr6:28334200-28345600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr6:28334200-28346000	Weak transcription	Fetal Intestine Small	intestine
45	chr6:28334200-28346000	Weak transcription	HMEC	breast
46	chr6:28334200-28346200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr6:28334200-28347800	Weak transcription	NHLF	lung
48	chr6:28334200-28348000	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr6:28334200-28348000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr6:28334200-28348200	Weak transcription	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links