Variant report

Variant	rs7552104
Chromosome Location	chr1:94213626-94213627
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:93818955..93820839-chr1:94212992..94214786,2	K562	blood:
2	chr1:94206892..94209367-chr1:94213428..94215189,2	MCF-7	breast:
3	chr1:94213369..94215810-chr1:94218586..94221367,2	MCF-7	breast:
4	chr1:94207201..94209502-chr1:94212194..94214368,2	K562	blood:

Variant related genes	Relation type
ENSG00000117505	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1004197	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11164975	0.89[JPT][hapmap]
rs11164976	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs11164979	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs11164984	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs11164986	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs11165004	0.86[CHB][hapmap]
rs11165006	0.83[CHB][hapmap]
rs11165007	0.86[CHB][hapmap]
rs11165012	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11165016	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11800779	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs12125068	0.86[CHB][hapmap]
rs12125652	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12126518	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs12128353	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs12129080	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs12132181	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs12132405	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs12132569	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs12132625	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs12134159	0.86[CHB][hapmap]
rs12135187	0.86[CHB][hapmap]
rs12139561	0.86[CHB][hapmap]
rs12139968	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs12140014	0.86[CHB][hapmap]
rs12142384	0.86[CHB][hapmap]
rs12144277	0.86[CHB][hapmap]
rs12240145	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs12402802	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs12404613	0.85[JPT][hapmap]
rs12405302	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs12406885	0.86[CHB][hapmap]
rs12407244	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs12407550	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs12407732	0.84[CHB][hapmap]
rs12407917	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs12408089	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs12408109	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs12408402	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs12408797	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs12410342	0.84[CHB][hapmap]
rs12410985	0.92[CHB][hapmap];0.89[JPT][hapmap]
rs12410986	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs12411043	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs12411056	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs12725087	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs12745866	0.88[JPT][hapmap]
rs12745888	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs17100392	0.86[CHB][hapmap]
rs1848	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs1852	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs1980084	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs2179908	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2391313	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3935320	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs3935334	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs4075343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4281327	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs4348734	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs4354545	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs4357541	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs6541395	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs6541396	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6661992	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6662311	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6679619	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6684128	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs6684389	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs6687914	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6688926	0.86[CHB][hapmap]
rs6691888	0.89[JPT][hapmap]
rs6692107	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs6692717	0.84[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs6702162	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs717912	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs7515462	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7521365	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7536914	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7537445	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7544883	0.86[CHB][hapmap]
rs7546315	0.86[CHB][hapmap]
rs7547179	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs960625	0.86[CHB][hapmap]
rs9729722	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3320426	chr1:94212708-94213724	Weak transcription Enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	esv3320425	chr1:94212773-94213635	Weak transcription Enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	esv3320427	chr1:94212773-94213635	ZNF genes & repeats Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv10207	chr1:94212859-94213642	Weak transcription ZNF genes & repeats Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7552104	GCLM	cis	parietal	SCAN
rs7552104	GCLM	Cis_1M	lymphoblastoid	RTeQTL
rs7552104	LRRC8B	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94199400-94217400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:94208200-94215600	Weak transcription	Aorta	Aorta
3	chr1:94210800-94215600	Weak transcription	Thymus	Thymus
4	chr1:94211800-94215600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:94212400-94214400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:94212600-94215200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:94212600-94217200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:94213000-94216200	Weak transcription	Esophagus	oesophagus
9	chr1:94213200-94216800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:94213400-94215600	Weak transcription	HMEC	breast
11	chr1:94213400-94217800	Enhancers	Primary B cells from peripheral blood	blood
12	chr1:94213600-94215400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:94213600-94215600	Weak transcription	HepG2	liver

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