Variant report

Variant	rs12127432
Chromosome Location	chr1:85095457-85095458
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:85094796..85097662-chr1:85099991..85101818,2	K562	blood:
2	chr1:85094114..85095940-chr1:85097671..85099703,2	MCF-7	breast:
3	chr1:85094581..85097070-chr1:85122800..85125506,2	K562	blood:
4	chr1:85087934..85091159-chr1:85092418..85095457,3	K562	blood:
5	chr1:85094176..85096691-chr1:85103234..85105351,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C1orf180-2	chr1:85093913-85096570	NR_027379

Variant related genes	Relation type
ENSG00000180869	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11578078	0.85[CHB][hapmap];0.92[JPT][hapmap]
rs12022113	0.85[CHB][hapmap];0.92[JPT][hapmap]
rs12123923	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12125951	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2298076	0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2911567	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2911571	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs2911611	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2943672	1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2994429	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs2994437	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2994439	0.81[ASN][1000 genomes]
rs2994440	0.81[ASN][1000 genomes]
rs2994941	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2994949	0.92[CHB][hapmap];0.80[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3096445	0.80[CEU][hapmap];0.92[CHB][hapmap]
rs3768238	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap]
rs3782	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6576722	0.89[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap]
rs6576723	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs6682889	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs6687220	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs7545555	0.82[ASN][1000 genomes]
rs9661716	0.92[CHB][hapmap];0.92[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1000325	chr1:85032605-85100748	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85086800-85098400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:85086800-85100000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:85087000-85147400	Weak transcription	Gastric	stomach

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