Variant report

Variant	rs12648523
Chromosome Location	chr4:85492698-85492699
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:85485621..85488244-chr4:85490405..85493173,2	MCF-7	breast:
2	chr4:85490056..85493038-chr4:85496347..85498116,2	MCF-7	breast:
3	chr4:85483142..85485554-chr4:85491357..85493082,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1020278	0.85[CEU][hapmap];0.83[MEX][hapmap];0.82[EUR][1000 genomes]
rs10446695	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs10776519	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11097023	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11099651	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11099652	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11099653	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11725539	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11733870	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11929910	0.84[CEU][hapmap];0.83[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12509774	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13102661	0.94[GIH][hapmap];0.83[MEX][hapmap]
rs1372971	0.91[GIH][hapmap];0.92[MEX][hapmap]
rs1443074	0.94[GIH][hapmap]
rs2868914	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2868915	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2868916	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2868917	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2868919	0.85[CEU][hapmap];0.94[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs2868920	0.83[JPT][hapmap];0.83[MEX][hapmap]
rs35227341	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35909314	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4449405	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4533768	0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6535544	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6829806	0.91[GIH][hapmap];0.83[MEX][hapmap]
rs7657036	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7657224	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7659340	0.85[CEU][hapmap];0.83[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7677285	0.88[CEU][hapmap];0.81[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7678115	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7678268	0.82[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7699871	0.91[ASN][1000 genomes]
rs9784491	0.91[GIH][hapmap];0.83[MEX][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12648523	NCRNA00247	cis	cerebellum	SCAN
rs12648523	NKX6-1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:85489800-85503400	Weak transcription	Lung	lung
2	chr4:85490000-85494800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr4:85490000-85500400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr4:85490400-85494800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr4:85490600-85495000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr4:85490600-85495000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr4:85490600-85495000	Weak transcription	HSMMtube	muscle
8	chr4:85490600-85500200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr4:85490600-85500600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr4:85490600-85501200	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr4:85490800-85500200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr4:85491000-85493600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr4:85491000-85500000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr4:85491200-85493400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr4:85491200-85493400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr4:85491400-85493600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr4:85491400-85495000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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