Variant report

Variant	rs2994429
Chromosome Location	chr1:85175584-85175585
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:85156633..85159408-chr1:85174909..85176958,2	MCF-7	breast:
2	chr1:85156009..85157744-chr1:85174703..85176988,2	K562	blood:

Variant related genes	Relation type
ENSG00000117155	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11578078	0.92[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.90[ASN][1000 genomes]
rs12022113	0.92[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[ASN][1000 genomes]
rs12120614	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12123923	0.84[CHB][hapmap];0.92[JPT][hapmap]
rs12125951	0.92[CHB][hapmap];0.88[CHD][hapmap];0.92[JPT][hapmap]
rs12127432	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs1340527	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1340528	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2298076	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2911567	0.92[CHB][hapmap];0.91[CHD][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs2911571	0.92[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2911575	1.00[ASN][1000 genomes]
rs2911578	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2911583	0.97[ASN][1000 genomes]
rs2911611	0.93[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2943672	0.93[CEU][hapmap];0.92[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2994437	1.00[CHB][hapmap];0.91[CHD][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs2994439	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2994440	0.92[ASN][1000 genomes]
rs2994449	0.93[CEU][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2994941	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2994949	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3096445	1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[ASN][1000 genomes]
rs3768238	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3782	1.00[CHB][hapmap];0.91[CHD][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs4390189	1.00[ASN][1000 genomes]
rs4551615	1.00[ASN][1000 genomes]
rs56681543	0.98[ASN][1000 genomes]
rs6576722	1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6576723	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6670415	0.99[ASN][1000 genomes]
rs6670434	0.94[ASN][1000 genomes]
rs6682889	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6687220	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7524511	0.84[JPT][hapmap]
rs818525	0.83[ASN][1000 genomes]
rs9661716	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9662145	0.87[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2994429	LMO4	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85165200-85179000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:85167600-85177000	Weak transcription	Aorta	Aorta
3	chr1:85168400-85176800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr1:85168600-85176400	Weak transcription	Fetal Stomach	stomach
5	chr1:85170000-85177400	Weak transcription	Fetal Brain Female	brain
6	chr1:85171400-85176800	Weak transcription	Fetal Lung	lung
7	chr1:85171600-85177000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:85171600-85184400	Weak transcription	Fetal Kidney	kidney
9	chr1:85174000-85180400	Weak transcription	Stomach Smooth Muscle	stomach
10	chr1:85174200-85175600	Enhancers	K562	blood
11	chr1:85174200-85176800	Weak transcription	NHLF	lung
12	chr1:85174200-85177000	Weak transcription	Osteobl	bone
13	chr1:85174400-85176800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:85174800-85176800	Enhancers	Fetal Brain Male	brain
15	chr1:85175000-85176000	Enhancers	Fetal Intestine Small	intestine
16	chr1:85175000-85184200	Weak transcription	Fetal Intestine Large	intestine
17	chr1:85175400-85176000	Enhancers	Colon Smooth Muscle	Colon

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