Variant report

Variant	rs1048694
Chromosome Location	chr1:151669997-151669998
allele	A/C
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	chr1:151669952-151670400	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr1:151669394-151671424	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:151665857..151667838-chr1:151669687..151671495,2	K562	blood:
2	chr1:151665857..151667896-chr1:151669494..151672428,3	K562	blood:
3	chr1:151658558..151661445-chr1:151669676..151671900,2	K562	blood:
4	chr1:151668533..151670449-chr1:151674606..151677478,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000227045	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10888428	0.92[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11204866	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11586679	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1196350	0.80[MEX][hapmap]
rs1196352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1196357	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs1196459	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1196464	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1196465	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1201651	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1211981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12122920	0.84[MEX][hapmap]
rs1308137	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1308139	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1308143	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1308145	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1308146	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1308147	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1308148	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1308152	0.92[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1308158	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1717128	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17641780	0.92[CEU][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs1781434	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1891589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1891591	0.82[ASN][1000 genomes]
rs2460996	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2489892	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2495392	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2495393	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2495394	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3204344	0.96[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs35981950	0.83[EUR][1000 genomes]
rs3790512	0.92[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6684548	0.95[EUR][1000 genomes]
rs6685067	0.96[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs6687866	0.96[CEU][hapmap];0.98[EUR][1000 genomes]
rs6702842	0.95[CEU][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs7534887	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1048694	LINGO4	cis	cerebellum	SCAN
rs1048694	BCL9	cis	cerebellum	SCAN
rs1048694	TDRKH	cis	parietal	SCAN
rs1048694	LCE1C	cis	parietal	SCAN
rs1048694	TDRKH	cis	cerebellum	SCAN
rs1048694	PLEKHO1	cis	cerebellum	SCAN
rs1048694	S100A4	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151591200-151675400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr1:151627200-151670600	Weak transcription	Small Intestine	intestine
3	chr1:151627400-151676000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr1:151638600-151675600	Weak transcription	Psoas Muscle	Psoas
5	chr1:151653400-151671600	Weak transcription	Stomach Mucosa	stomach
6	chr1:151654800-151678000	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr1:151658000-151674800	Strong transcription	Fetal Muscle Leg	muscle
8	chr1:151660400-151675400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:151661600-151675400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr1:151662000-151670400	Weak transcription	Fetal Heart	heart
11	chr1:151663000-151675400	Strong transcription	Fetal Stomach	stomach
12	chr1:151663200-151677800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr1:151663200-151683200	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr1:151664200-151672800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:151664200-151674200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr1:151664200-151674600	Strong transcription	Primary T cells from cord blood	blood
17	chr1:151664200-151674800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:151664200-151675000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr1:151664400-151672200	Strong transcription	Fetal Intestine Small	intestine
20	chr1:151664400-151672400	Strong transcription	Fetal Intestine Large	intestine
21	chr1:151664400-151672400	Strong transcription	Thymus	Thymus
22	chr1:151664400-151674400	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr1:151664400-151674600	Strong transcription	Fetal Muscle Trunk	muscle
24	chr1:151664400-151674600	Strong transcription	Skeletal Muscle Female	skeletal muscle
25	chr1:151664400-151674800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:151664400-151675400	Strong transcription	Stomach Smooth Muscle	stomach
27	chr1:151664600-151674200	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr1:151664600-151674600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr1:151664600-151674600	Strong transcription	Fetal Thymus	thymus
30	chr1:151664600-151675000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr1:151664800-151672200	Strong transcription	Brain Germinal Matrix	brain
32	chr1:151664800-151674400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:151664800-151674600	Strong transcription	Adipose Nuclei	Adipose
34	chr1:151664800-151674600	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr1:151664800-151674800	Strong transcription	Spleen	Spleen
36	chr1:151665000-151670000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
37	chr1:151665000-151673200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr1:151665000-151673800	Strong transcription	Primary B cells from peripheral blood	blood
39	chr1:151665000-151673800	Strong transcription	Brain Cingulate Gyrus	brain
40	chr1:151665000-151674000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr1:151665000-151674000	Strong transcription	Dnd41	blood
42	chr1:151665000-151674200	Strong transcription	Duodenum Mucosa	Duodenum
43	chr1:151665000-151674400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:151665000-151674600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr1:151665000-151674600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr1:151665000-151674600	Strong transcription	Liver	Liver
47	chr1:151665000-151674600	Strong transcription	Fetal Lung	lung
48	chr1:151665000-151674600	Strong transcription	Lung	lung
49	chr1:151665000-151674800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:151665000-151674800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links