Variant report

Variant	rs7398021
Chromosome Location	chr12:51440473-51440474
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:51414500..51424231-chr12:51435741..51444321,19	K562	blood:
2	chr12:51440322..51443098-chr12:51662230..51665433,4	K562	blood:
3	chr12:51440271..51447226-chr12:51475135..51479930,16	MCF-7	breast:
4	chr12:51440439..51443022-chr12:51565659..51567306,3	K562	blood:
5	chr12:51418602..51423346-chr12:51439309..51444851,15	MCF-7	breast:
6	chr12:51439067..51445190-chr12:51449547..51456560,11	K562	blood:
7	chr12:51440111..51442560-chr12:51783834..51785722,2	MCF-7	breast:
8	chr12:51429499..51431522-chr12:51440148..51442114,3	MCF-7	breast:
9	chr12:51156477..51159239-chr12:51440349..51444629,5	K562	blood:
10	chr12:51416659..51422801-chr12:51440164..51444812,17	MCF-7	breast:
11	chr12:51438469..51440828-chr12:51713413..51715859,2	K562	blood:
12	chr12:51319328..51321939-chr12:51438898..51441573,2	K562	blood:

No data

No data

No data

Variant related genes	Relation type
ENSG00000139629	Chromatin interaction
ENSG00000110911	Chromatin interaction
ENSG00000123268	Chromatin interaction
ENSG00000135457	Chromatin interaction
ENSG00000110925	Chromatin interaction
ENSG00000199903	Chromatin interaction
ENSG00000170545	Chromatin interaction
ENSG00000050438	Chromatin interaction
ENSG00000050426	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1112391	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11169689	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11169690	0.85[ASN][1000 genomes]
rs11169691	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11169692	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2018022	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2306732	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3759405	0.85[AFR][1000 genomes]
rs55938119	0.86[EUR][1000 genomes]
rs66781280	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7722	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs970097	0.89[EUR][1000 genomes];0.80[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	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7398021	TFCP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51435600-51440800	Weak transcription	HepG2	liver
2	chr12:51436600-51440800	Weak transcription	Brain Hippocampus Middle	brain
3	chr12:51437600-51441000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:51437800-51440800	Weak transcription	Hela-S3	cervix
5	chr12:51438600-51441400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr12:51439600-51440800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr12:51439600-51441000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr12:51440400-51440800	Enhancers	GM12878-XiMat	blood

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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