Variant report

Variant	rs712518
Chromosome Location	chr3:111671862-111671863
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	GATA3	chr3:111671823-111672003	SH-SY5Y	brain:	n/a	chr3:111671843-111671859 chr3:111671846-111671855 chr3:111671848-111671855 chr3:111671848-111671855 chr3:111671848-111671855 chr3:111671841-111671862
2	GATA2	chr3:111671652-111672022	SH-SY5Y	brain:	n/a	chr3:111671843-111671859 chr3:111671846-111671855 chr3:111671848-111671855 chr3:111671848-111671855 chr3:111671848-111671855 chr3:111671841-111671862
3	POLR2A	chr3:111671652-111671965	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr3:111671455-111673754	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
PHLDB2	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11713044	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1282939	0.88[EUR][1000 genomes]
rs1282945	0.95[CEU][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1282946	1.00[JPT][hapmap]
rs13061421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16858936	1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4682066	0.89[CHB][hapmap];0.91[ASN][1000 genomes]
rs493456	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs579082	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6438024	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6796683	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6804475	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712514	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs712519	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs766745	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774744	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9816238	0.89[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9834695	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9839401	0.84[ASN][1000 genomes]
rs9867058	0.86[CHB][hapmap];1.00[JPT][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs712518	QTRTD1	cis	parietal	SCAN
rs712518	CD200R1L	cis	parietal	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111631000-111672000	Weak transcription	Fetal Intestine Small	intestine
2	chr3:111631000-111673400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr3:111637200-111690600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:111639200-111675400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:111642200-111674400	Weak transcription	Lung	lung
6	chr3:111642200-111690400	Weak transcription	Spleen	Spleen
7	chr3:111645400-111689600	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr3:111648600-111674800	Weak transcription	Psoas Muscle	Psoas
9	chr3:111652400-111685800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr3:111653000-111686200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr3:111654400-111695000	Strong transcription	Placenta	Placenta
12	chr3:111656600-111672000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr3:111656600-111673200	Weak transcription	Stomach Mucosa	stomach
14	chr3:111656600-111674600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr3:111656600-111679200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:111657200-111672600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr3:111657200-111682000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:111657400-111673000	Strong transcription	Osteobl	bone
19	chr3:111657800-111674600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:111658000-111673000	Strong transcription	Adipose Nuclei	Adipose
21	chr3:111658000-111673200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:111658600-111697400	Weak transcription	Gastric	stomach
23	chr3:111658800-111672600	Weak transcription	Fetal Kidney	kidney
24	chr3:111658800-111685800	Weak transcription	HepG2	liver
25	chr3:111660400-111672400	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr3:111660600-111672400	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr3:111660800-111672000	Weak transcription	Fetal Intestine Large	intestine
28	chr3:111661000-111676000	Weak transcription	Duodenum Mucosa	Duodenum
29	chr3:111661600-111689800	Weak transcription	Ovary	ovary
30	chr3:111662000-111672600	Weak transcription	Aorta	Aorta
31	chr3:111663000-111672200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr3:111663000-111681400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr3:111663200-111675200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr3:111663800-111681200	Strong transcription	NHEK	skin
35	chr3:111664000-111673400	Strong transcription	HMEC	breast
36	chr3:111664600-111672600	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr3:111664800-111672400	Weak transcription	Right Ventricle	heart
38	chr3:111665800-111675400	Weak transcription	Right Atrium	heart
39	chr3:111666000-111672400	Weak transcription	Rectal Smooth Muscle	rectum
40	chr3:111666600-111675200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr3:111666600-111697400	Weak transcription	Esophagus	oesophagus
42	chr3:111667000-111675400	Strong transcription	HSMM	muscle
43	chr3:111667200-111675200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr3:111667800-111672400	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr3:111668000-111672000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr3:111668000-111672400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:111669000-111672400	Weak transcription	Fetal Lung	lung
48	chr3:111670800-111685000	Strong transcription	Liver	Liver
49	chr3:111671000-111672000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr3:111671000-111672600	Strong transcription	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links