Variant report

Variant	rs9370246
Chromosome Location	chr6:53804736-53804737
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:53802203..53805380-chr6:53806061..53808380,3	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1076701	0.89[ASW][hapmap];1.00[CEU][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1076702	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12526194	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2073020	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2076495	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2294789	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2294790	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2294791	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3777661	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4400206	0.82[MEX][hapmap]
rs4455653	0.81[ASN][1000 genomes]
rs4516937	0.86[JPT][hapmap];0.82[MEX][hapmap]
rs4563705	0.88[JPT][hapmap]
rs6934324	0.84[JPT][hapmap]
rs7763482	0.86[JPT][hapmap];0.82[MEX][hapmap]
rs9349685	0.93[CEU][hapmap]
rs9357776	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9357778	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9370233	0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs9370241	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9370244	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9370247	0.83[AFR][1000 genomes]
rs9370248	0.83[AFR][1000 genomes]
rs9382235	0.86[JPT][hapmap]
rs9382243	0.94[CEU][hapmap];0.82[MEX][hapmap]
rs9382252	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9382253	0.82[EUR][1000 genomes]
rs9382254	0.94[CEU][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs9382256	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9382257	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9382258	0.83[AFR][1000 genomes]
rs9382259	0.83[AFR][1000 genomes]
rs9395878	0.94[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs9474646	0.86[JPT][hapmap]

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	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	nsv830664	chr6:53698021-53825270	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1067663	chr6:53796341-54449718	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv529158	chr6:53796341-54449718	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9370246	LRRC1	cis	parietal	SCAN
rs9370246	MRPS31	trans	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53787800-53807800	Weak transcription	Aorta	Aorta
2	chr6:53787800-53810800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:53794600-53807800	Weak transcription	Left Ventricle	heart
4	chr6:53794800-53815600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:53795200-53807400	Weak transcription	Fetal Stomach	stomach
6	chr6:53795600-53826200	Weak transcription	NHEK	skin
7	chr6:53799800-53810600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:53803200-53805000	Enhancers	Dnd41	blood
9	chr6:53803800-53807400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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