Variant report

Variant	rs7544801
Chromosome Location	chr1:179005970-179005971
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF263	chr1:179005826-179006432	HEK293-T-REx	kidney:	n/a	n/a

Variant related genes	Relation type
ENSG00000232750	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10082052	0.93[CEU][hapmap];0.81[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10458367	0.81[AMR][1000 genomes]
rs1046385	1.00[ASW][hapmap];0.80[CEU][hapmap];0.90[GIH][hapmap];0.80[TSI][hapmap]
rs10798649	0.81[JPT][hapmap]
rs10913672	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11581232	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1325194	1.00[ASW][hapmap]
rs2025584	0.84[JPT][hapmap]
rs2182102	0.80[AMR][1000 genomes]
rs2296377	0.81[CHB][hapmap];0.85[GIH][hapmap];0.83[AMR][1000 genomes]
rs2636266	1.00[ASW][hapmap]
rs2636290	1.00[ASW][hapmap];0.81[MEX][hapmap]
rs2793805	1.00[ASW][hapmap]
rs28913887	1.00[YRI][hapmap]
rs28913889	1.00[YRI][hapmap]
rs3753533	0.81[JPT][hapmap]
rs3813638	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3818433	1.00[ASW][hapmap]
rs3820163	0.81[JPT][hapmap]
rs4360489	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4652344	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4652348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6425512	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6425515	0.82[CEU][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs6697029	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7532578	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7538498	0.95[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7544801	RALGPS2	cis	parietal	SCAN
rs7544801	GPR52	cis	parietal	SCAN
rs7544801	TOR3A	cis	Artery Tibial	GTEx
rs7544801	FAM20B	cis	parietal	SCAN
rs7544801	FAM20B	cis	Artery Tibial	GTEx
rs7544801	FAM20B	cis	cerebellum	SCAN
rs7544801	ABL2	cis	parietal	SCAN
rs7544801	TOR3A	cis	multi-tissue	Pritchard

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:178996200-179009200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:178996400-179006200	Weak transcription	Fetal Stomach	stomach
3	chr1:178996400-179011200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:178998200-179008600	Enhancers	Colon Smooth Muscle	Colon
5	chr1:178998400-179027400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:178998600-179006000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:178998600-179007600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr1:178998600-179008000	Weak transcription	Placenta	Placenta
9	chr1:178999000-179009600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:179000000-179006200	Weak transcription	Fetal Intestine Small	intestine
11	chr1:179001200-179008600	Enhancers	Primary B cells from peripheral blood	blood
12	chr1:179001200-179009600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr1:179001400-179007600	Weak transcription	Fetal Brain Female	brain
14	chr1:179001600-179017000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr1:179001800-179008600	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr1:179001800-179016200	Weak transcription	Aorta	Aorta
17	chr1:179002000-179019200	Weak transcription	Adipose Nuclei	Adipose
18	chr1:179002200-179007600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:179002800-179008600	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr1:179003200-179008600	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr1:179003400-179007200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:179003600-179006000	Weak transcription	Esophagus	oesophagus
23	chr1:179003600-179007200	Weak transcription	Ovary	ovary
24	chr1:179003600-179009200	Weak transcription	Right Ventricle	heart
25	chr1:179003800-179006000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr1:179003800-179011200	Weak transcription	Thymus	Thymus
27	chr1:179003800-179025800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr1:179004000-179007600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr1:179004000-179008000	Enhancers	NHDF-Ad	bronchial
30	chr1:179004000-179011000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:179004200-179006200	Weak transcription	HSMMtube	muscle
32	chr1:179004200-179006400	Flanking Active TSS	GM12878-XiMat	blood
33	chr1:179004200-179007600	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr1:179004200-179007600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr1:179004200-179007800	Weak transcription	Brain Anterior Caudate	brain
36	chr1:179004200-179009200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr1:179004200-179010800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr1:179004200-179024200	Weak transcription	Liver	Liver
39	chr1:179004400-179006000	Active TSS	Stomach Smooth Muscle	stomach
40	chr1:179004400-179006000	Weak transcription	NH-A	brain
41	chr1:179004400-179006400	Weak transcription	Hela-S3	cervix
42	chr1:179004400-179007200	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr1:179004400-179007200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr1:179004400-179007400	Weak transcription	HepG2	liver
45	chr1:179004400-179007600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr1:179004400-179007600	Weak transcription	Fetal Heart	heart
47	chr1:179004400-179008200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr1:179004400-179012800	Weak transcription	Fetal Lung	lung
49	chr1:179004400-179013000	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr1:179004400-179019200	Weak transcription	Duodenum Mucosa	Duodenum

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