Variant report

Variant	rs1225140
Chromosome Location	chr11:76553731-76553732
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:76551458..76554014-chr11:76570616..76573436,2	MCF-7	breast:
2	chr11:76545387..76548073-chr11:76553692..76555728,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000078124	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10793220	0.89[GIH][hapmap]
rs10899310	0.87[GIH][hapmap]
rs1149577	0.84[EUR][1000 genomes]
rs1149626	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs1224951	0.85[EUR][1000 genomes]
rs1224952	0.83[EUR][1000 genomes]
rs1225127	0.85[EUR][1000 genomes]
rs1225129	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1225131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1225132	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1225133	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1225134	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1225135	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1225136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1225137	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1225139	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1225141	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1225144	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1225147	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1225149	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12291376	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1234832	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1235157	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12718490	0.89[GIH][hapmap]
rs12794575	0.80[CEU][hapmap]
rs12796913	0.87[GIH][hapmap]
rs1356455	0.89[GIH][hapmap]
rs1372045	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1372046	0.87[CEU][hapmap]
rs1474087	0.87[GIH][hapmap]
rs1517907	0.81[CEU][hapmap]
rs1660579	1.00[CEU][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs2119455	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2119457	0.89[GIH][hapmap]
rs2451908	0.80[EUR][1000 genomes]
rs4379869	0.89[GIH][hapmap]
rs4457775	0.81[CEU][hapmap]
rs4471450	0.89[GIH][hapmap]
rs4488228	0.89[GIH][hapmap]
rs4944132	0.80[CEU][hapmap]
rs591043	0.87[CEU][hapmap]
rs6592671	0.88[CEU][hapmap];0.92[GIH][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs6592680	0.89[GIH][hapmap]
rs7106625	0.89[GIH][hapmap]
rs7113282	0.89[GIH][hapmap]
rs7113290	0.81[CEU][hapmap];0.89[GIH][hapmap]
rs7117545	0.89[GIH][hapmap]
rs7117682	0.89[GIH][hapmap]
rs7118762	0.89[GIH][hapmap]
rs7119361	0.89[GIH][hapmap]
rs7924613	0.86[CEU][hapmap]
rs7925135	0.81[CEU][hapmap]
rs7927367	0.85[CEU][hapmap]
rs7927658	0.89[GIH][hapmap]
rs7931561	0.81[CEU][hapmap];0.89[GIH][hapmap]
rs7932288	0.81[CEU][hapmap];0.89[GIH][hapmap]
rs7937883	0.86[GIH][hapmap]
rs7942574	0.89[GIH][hapmap]
rs894065	0.89[AFR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs920512	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs938810	0.89[GIH][hapmap]

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1225140	CAPN5	cis	parietal	SCAN
rs1225140	ACER3	cis	cerebellum	SCAN
rs1225140	GDPD5	cis	parietal	SCAN
rs1225140	ACER3	cis	lymphoblastoid	seeQTL
rs1225140	ACER3	cis	parietal	SCAN
rs1225140	NEU3	cis	parietal	SCAN
rs1225140	ODZ4	cis	parietal	SCAN
rs1225140	LIPT2	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:76549600-76561000	Weak transcription	Right Atrium	heart
2	chr11:76549600-76570800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:76549800-76572000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr11:76550600-76566400	Weak transcription	Lung	lung
5	chr11:76551200-76555400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr11:76551600-76555200	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr11:76551600-76558400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr11:76551800-76555600	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr11:76552400-76553800	Enhancers	Liver	Liver
10	chr11:76553000-76553800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr11:76553200-76553800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr11:76553400-76560400	Weak transcription	K562	blood
13	chr11:76553600-76553800	Enhancers	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links