Variant report

Variant	rs1481824
Chromosome Location	chr4:54241402-54241403
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	TCF7L2	chr4:54241322-54241659	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:54230756..54233682-chr4:54240977..54245711,5	MCF-7	breast:
2	chr4:54231715..54234430-chr4:54240716..54243244,3	MCF-7	breast:
3	chr4:54241165..54243159-chr4:54244086..54246156,2	MCF-7	breast:

Variant related genes	Relation type
FIP1L1	TF binding region
ENSG00000145216	Chromatin interaction
ENSG00000184178	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10000746	1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10001201	0.86[CEU][hapmap];0.88[EUR][1000 genomes]
rs10007903	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs10011259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10017903	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10021541	0.88[EUR][1000 genomes]
rs10028142	0.82[EUR][1000 genomes]
rs1021099	0.88[EUR][1000 genomes]
rs11133266	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11722866	0.83[EUR][1000 genomes]
rs11723755	0.83[EUR][1000 genomes]
rs11725230	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs11731499	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11734039	0.86[CEU][hapmap];0.88[EUR][1000 genomes]
rs11734681	0.82[CEU][hapmap]
rs11947256	0.88[EUR][1000 genomes]
rs12507563	0.82[CEU][hapmap]
rs12507739	0.82[CEU][hapmap]
rs12508701	0.82[CEU][hapmap]
rs12511088	0.82[CEU][hapmap]
rs12511253	0.81[CEU][hapmap]
rs12642403	0.82[CEU][hapmap]
rs12649718	0.88[EUR][1000 genomes]
rs12651390	0.86[CEU][hapmap]
rs1471597	0.88[EUR][1000 genomes]
rs1481819	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1531748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1600795	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17082782	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17082893	0.82[CEU][hapmap]
rs17520800	0.82[EUR][1000 genomes]
rs2090117	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2271554	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271559	0.81[CEU][hapmap]
rs2412447	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2412488	0.83[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];0.97[TSI][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28414913	0.82[EUR][1000 genomes]
rs28579268	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35499169	0.87[EUR][1000 genomes]
rs3765158	0.83[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[TSI][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3811782	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3811785	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs4864759	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4864760	0.86[CEU][hapmap];0.88[EUR][1000 genomes]
rs4864767	0.82[CEU][hapmap]
rs56998298	0.88[EUR][1000 genomes]
rs6554100	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6554104	0.86[CEU][hapmap];0.88[EUR][1000 genomes]
rs6554105	0.86[CEU][hapmap];0.88[EUR][1000 genomes]
rs6554106	0.83[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];0.97[TSI][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6818788	0.82[CEU][hapmap]
rs6822201	0.82[CEU][hapmap]
rs6825364	0.81[EUR][1000 genomes]
rs6827269	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6828559	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs6833766	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs6834934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6838260	0.82[CEU][hapmap]
rs6839922	0.82[CEU][hapmap]
rs6840530	0.82[CEU][hapmap]
rs6848887	0.87[EUR][1000 genomes]
rs6852884	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6857024	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6857869	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7655975	0.88[EUR][1000 genomes]
rs7682199	0.80[EUR][1000 genomes]
rs7686177	0.80[EUR][1000 genomes]
rs7686876	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7689981	0.82[EUR][1000 genomes]
rs7690908	0.82[EUR][1000 genomes]
rs7691578	0.83[EUR][1000 genomes]
rs7697622	0.88[EUR][1000 genomes]
rs7698792	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs931181	0.86[CEU][hapmap];0.88[EUR][1000 genomes]
rs931182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9312639	0.82[EUR][1000 genomes]
rs980987	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9995284	0.81[EUR][1000 genomes]
rs9996883	0.82[CEU][hapmap]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1481824	LYRM5	trans	cerebellum	SCAN
rs1481824	EXOC1	cis	cerebellum	SCAN
rs1481824	TYW1B	trans	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54233000-54243200	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr4:54238600-54243000	Weak transcription	K562	blood
3	chr4:54239200-54242200	Weak transcription	Colonic Mucosa	Colon
4	chr4:54240200-54243200	Weak transcription	HSMMtube	muscle
5	chr4:54241200-54242200	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr4:54241200-54243200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr4:54241400-54243200	Enhancers	Stomach Mucosa	stomach
8	chr4:54241400-54243600	Weak transcription	Gastric	stomach

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