Variant report

Variant	rs12216441
Chromosome Location	chr6:53633422-53633423
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	chr6:53617168..53619456-chr6:53632557..53635306,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10456165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10456673	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10456674	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10948768	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10948782	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap]
rs11962552	1.00[CEU][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11968082	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12192118	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12195491	1.00[CHB][hapmap]
rs12202762	1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12204130	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211417	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211478	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211680	0.86[JPT][hapmap]
rs12213392	0.86[JPT][hapmap]
rs12213577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[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	0.88[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17748374	0.81[ASN][1000 genomes]
rs34113003	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34876933	0.98[AMR][1000 genomes];0.97[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];0.95[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4639324	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap]
rs55931905	0.87[ASN][1000 genomes]
rs72941941	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7762326	0.81[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12216441	LRRC1	Cis_1M	lymphoblastoid	RTeQTL
rs12216441	LRRC1	cis	parietal	SCAN

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	chr6:53618800-53635800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:53629400-53633600	Enhancers	HSMMtube	muscle
4	chr6:53630400-53634400	Weak transcription	Placenta	Placenta
5	chr6:53630400-53634800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:53632000-53636000	Weak transcription	Aorta	Aorta
7	chr6:53632000-53639600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr6:53632200-53635400	Weak transcription	Fetal Heart	heart
9	chr6:53632200-53639000	Weak transcription	Gastric	stomach
10	chr6:53632800-53633800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:53632800-53633800	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr6:53633400-53633600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr6:53633400-53633600	Weak transcription	Fetal Muscle Leg	muscle
14	chr6:53633400-53633800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr6:53633400-53634200	Enhancers	NHEK	skin

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