Variant report

Variant	rs4537578
Chromosome Location	chr1:85121255-85121256
allele	C/T
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	POLR2A	chr1:85121087-85122199	K562	blood:	n/a	n/a
2	JUN	chr1:85121108-85121451	K562	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C1orf180-5	chr1:85121001-85121271	NONHSAT004228

Variant related genes	Relation type
SSX2IP	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10218582	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10465723	0.84[ASN][1000 genomes]
rs1057746	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10874453	0.82[CEU][hapmap];0.80[CHB][hapmap];0.88[JPT][hapmap]
rs10874454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161435	0.90[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs11161436	0.90[CHB][hapmap];0.81[CHD][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs11164031	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11164032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164033	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164034	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11164036	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11164041	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11164048	0.84[CEU][hapmap];0.90[CHB][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12044089	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12049262	0.89[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12137124	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12730273	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12736243	0.81[AMR][1000 genomes]
rs2911561	0.93[ASN][1000 genomes]
rs2911562	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[ASN][1000 genomes]
rs2911563	0.89[ASN][1000 genomes]
rs2911564	0.88[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs2911565	0.91[ASN][1000 genomes]
rs2911566	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3118466	0.83[ASN][1000 genomes]
rs3768239	1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.91[ASN][1000 genomes]
rs3768240	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3768241	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3768242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3768243	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4907086	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs57636989	0.84[ASN][1000 genomes]
rs6681911	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7524511	0.87[CHB][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7550108	0.83[ASN][1000 genomes]
rs818524	0.84[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4537578	LPAR3	cis	parietal	SCAN
rs4537578	SH3GLB1	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85087000-85147400	Weak transcription	Gastric	stomach
2	chr1:85099000-85123400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:85099200-85121400	Weak transcription	NHDF-Ad	bronchial
4	chr1:85099200-85138200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr1:85099400-85131200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:85099600-85122600	Weak transcription	Fetal Brain Male	brain
7	chr1:85101000-85123200	Weak transcription	Fetal Kidney	kidney
8	chr1:85101000-85124400	Weak transcription	Hela-S3	cervix
9	chr1:85106200-85140400	Weak transcription	NHEK	skin
10	chr1:85106400-85155400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:85108000-85123200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr1:85108000-85155000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:85108200-85123400	Weak transcription	Esophagus	oesophagus
14	chr1:85108200-85128800	Weak transcription	GM12878-XiMat	blood
15	chr1:85108400-85121400	Weak transcription	Left Ventricle	heart
16	chr1:85108400-85121600	Weak transcription	Brain Germinal Matrix	brain
17	chr1:85109200-85133000	Weak transcription	Pancreas	Pancrea
18	chr1:85109600-85123200	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr1:85110200-85123000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:85110400-85121400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr1:85110800-85129400	Strong transcription	Fetal Thymus	thymus
22	chr1:85111200-85123800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr1:85111400-85128400	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr1:85111400-85131400	Weak transcription	HSMM	muscle
25	chr1:85111600-85123600	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr1:85111600-85127800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr1:85111800-85152000	Weak transcription	Aorta	Aorta
28	chr1:85112400-85129000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:85112400-85138200	Strong transcription	K562	blood
30	chr1:85112600-85130600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr1:85113000-85131200	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr1:85113200-85123200	Weak transcription	A549	lung
33	chr1:85113200-85138200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr1:85113400-85129200	Weak transcription	Fetal Heart	heart
35	chr1:85113400-85138200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr1:85113600-85121800	Weak transcription	HepG2	liver
37	chr1:85113800-85123400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr1:85113800-85126600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr1:85114000-85122400	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr1:85114200-85126600	Weak transcription	NH-A	brain
41	chr1:85114400-85123400	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr1:85114400-85124000	Weak transcription	Rectal Smooth Muscle	rectum
43	chr1:85114400-85127600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr1:85114400-85130800	Weak transcription	Ovary	ovary
45	chr1:85114400-85139000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr1:85114600-85124200	Weak transcription	Brain Angular Gyrus	brain
47	chr1:85114600-85130800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:85114800-85122400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr1:85114800-85128000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr1:85114800-85128600	Strong transcription	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links