Variant report

Variant	rs651298
Chromosome Location	chr1:70599458-70599459
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr1:70598373-70599501	SK-N-SH	brain:	n/a	chr1:70598805-70598824 chr1:70598807-70598814

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:70597641..70600279-chr1:70669633..70672162,2	MCF-7	breast:
2	chr1:70597842..70600180-chr1:70601599..70604524,2	K562	blood:

Variant related genes	Relation type
LRRC7	TF binding region
ENSG00000033122	Chromatin interaction
ENSG00000066557	Chromatin interaction
ENSG00000116754	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs626289	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs628249	0.85[AMR][1000 genomes]
rs631167	0.95[MEX][hapmap]
rs641909	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[MKK][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs654025	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs656448	0.87[AMR][1000 genomes]
rs657728	0.90[MEX][hapmap]
rs6688085	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7547666	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs826900	0.83[AMR][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	nsv531879	chr1:70386455-70644617	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1005397	chr1:70598803-70634585	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs651298	SERBP1	cis	cerebellum	SCAN
rs651298	NEGR1	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70557000-70599600	Weak transcription	Fetal Brain Female	brain
2	chr1:70583800-70599600	Weak transcription	Fetal Heart	heart
3	chr1:70596800-70609200	Weak transcription	Liver	Liver
4	chr1:70598400-70601200	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr1:70598800-70599800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:70598800-70600200	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr1:70598800-70600200	Enhancers	NHLF	lung
8	chr1:70598800-70601200	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr1:70599000-70600400	Enhancers	H1 Cell Line	embryonic stem cell
10	chr1:70599000-70600400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:70599000-70600400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr1:70599000-70606000	Weak transcription	Osteobl	bone
13	chr1:70599000-70606600	Weak transcription	K562	blood
14	chr1:70599000-70609600	Weak transcription	GM12878-XiMat	blood
15	chr1:70599200-70599600	Weak transcription	Brain Germinal Matrix	brain
16	chr1:70599200-70599600	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr1:70599200-70600000	Weak transcription	Hela-S3	cervix
18	chr1:70599200-70600200	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr1:70599200-70600400	Enhancers	NHDF-Ad	bronchial
20	chr1:70599400-70599600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:70599400-70600200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:70599400-70600400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:70599400-70601200	Enhancers	iPS-18 Cell Line	embryonic stem cell

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