Variant report

Variant	rs12202762
Chromosome Location	chr6:53610315-53610316
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:53610265..53615014-chr6:53656858..53662694,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228614	Chromatin interaction
ENSG00000137269	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10456165	1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10456673	1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10456674	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10948768	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10948782	1.00[CHB][hapmap]
rs11962552	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11968082	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12192118	1.00[CHB][hapmap]
rs12195491	1.00[CHB][hapmap]
rs12204130	1.00[CHB][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211417	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211478	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12213577	1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12216441	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13205690	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13211528	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17748374	0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs34113003	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34876933	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35078422	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35143842	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35868455	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35971619	0.87[ASN][1000 genomes]
rs4373362	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4639324	1.00[CHB][hapmap]
rs55931905	0.87[ASN][1000 genomes]
rs72941941	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7762326	0.84[AFR][1000 genomes];0.81[ASN][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	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1021506	chr6:53600338-53770482	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12202762	LRRC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53601600-53638000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr6:53601800-53613400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr6:53602200-53614800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr6:53606400-53611200	Weak transcription	HepG2	liver
5	chr6:53606400-53619600	Weak transcription	Right Atrium	heart
6	chr6:53606600-53611400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr6:53608600-53610800	Enhancers	Placenta	Placenta
8	chr6:53609000-53612200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr6:53609800-53611000	Enhancers	Esophagus	oesophagus
10	chr6:53610200-53610600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:53610200-53610600	Weak transcription	HMEC	breast
12	chr6:53610200-53610600	Weak transcription	NHEK	skin
13	chr6:53610200-53611600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:53610200-53611600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr6:53610200-53614000	Weak transcription	Placenta Amnion	Placenta Amnion

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