Variant report

No.	Distal block	Cell Line	Cell type
1	chr1:168872791..168875183-chr1:168876465..168878195,2	MCF-7	breast:
2	chr1:168872513..168874576-chr1:168888387..168891154,2	MCF-7	breast:
3	chr1:168847706..168850516-chr1:168873676..168876740,3	MCF-7	breast:
4	chr1:168873646..168880836-chr1:169073615..169079308,19	MCF-7	breast:
5	chr1:168871569..168873454-chr1:168873688..168876243,2	MCF-7	breast:
6	chr1:168872707..168877840-chr1:169073874..169079301,15	MCF-7	breast:
7	chr1:168848598..168851382-chr1:168873241..168874804,2	K562	blood:

Variant related genes	Relation type
ENSG00000143153	Chromatin interaction

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1028642	0.82[CEU][hapmap]
rs10919013	0.85[CEU][hapmap]
rs11577020	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[EUR][1000 genomes]
rs11586213	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12033844	0.84[EUR][1000 genomes]
rs12124802	0.92[EUR][1000 genomes]
rs12139484	0.92[EUR][1000 genomes]
rs1322493	0.80[EUR][1000 genomes]
rs1322494	0.80[EUR][1000 genomes]
rs1322496	0.84[EUR][1000 genomes]
rs1540942	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17571933	0.80[EUR][1000 genomes]
rs1819187	0.92[ASN][1000 genomes]
rs2065128	0.88[JPT][hapmap]
rs2104191	0.96[EUR][1000 genomes]
rs2146205	0.85[CEU][hapmap]
rs2208748	0.80[EUR][1000 genomes]
rs2208749	0.80[EUR][1000 genomes]
rs59148528	0.95[EUR][1000 genomes]
rs6427156	1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[YRI][hapmap];0.89[ASN][1000 genomes]
rs6660196	0.86[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs72695642	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7551577	0.88[JPT][hapmap];0.86[YRI][hapmap];0.89[ASN][1000 genomes]
rs973608	1.00[JPT][hapmap];0.80[TSI][hapmap]
rs992055	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869415	chr1:168467284-169153863	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
2	nsv437258	chr1:168824111-168890420	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2146204	POGK	cis	cerebellum	SCAN
rs2146204	POU2F1	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:168862400-168877000	Weak transcription	Fetal Heart	heart
2	chr1:168867000-168875600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:168868400-168876400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:168872800-168875000	Weak transcription	Pancreas	Pancrea
5	chr1:168872800-168875600	Weak transcription	Small Intestine	intestine
6	chr1:168872800-168875800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:168872800-168876600	Weak transcription	Esophagus	oesophagus
8	chr1:168873000-168875600	Weak transcription	HMEC	breast
9	chr1:168873000-168876000	Weak transcription	NHEK	skin
10	chr1:168873000-168876800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

Quick Search: