Variant report

Variant	rs11993947
Chromosome Location	chr8:124971455-124971456
allele	G/T
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:124968963..124971548-chr8:124973335..124975259,2	MCF-7	breast:
2	chr8:124971159..124973956-chr8:124976304..124978202,2	MCF-7	breast:
3	chr8:124968346..124974202-chr8:124988227..124995035,8	MCF-7	breast:
4	chr8:124964548..124966868-chr8:124970890..124973539,2	K562	blood:
5	chr8:124779816..124782654-chr8:124968951..124972407,3	MCF-7	breast:
6	chr8:124552529..124555386-chr8:124969535..124971577,2	MCF-7	breast:
7	chr8:124969317..124972187-chr8:124973160..124976482,5	MCF-7	breast:
8	chr8:124969536..124971932-chr8:124978093..124981369,4	MCF-7	breast:

No data

No data

No data

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10102622	0.92[CEU][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10282751	1.00[CEU][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10956157	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17270769	0.88[CEU][hapmap];0.92[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28620189	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4391416	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4870884	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4871445	0.94[CHB][hapmap];0.85[CHD][hapmap]
rs4871450	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6981430	0.84[CEU][hapmap];0.95[MEX][hapmap];0.84[EUR][1000 genomes]
rs6982889	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6986596	0.94[CHB][hapmap]
rs7004554	0.81[ASW][hapmap];1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7008604	1.00[CEU][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7465258	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs951247	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033617	chr8:124895516-125012783	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1035035	chr8:124895516-125020472	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv612141	chr8:124895809-125006490	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv612142	chr8:124896389-125006490	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv612143	chr8:124927711-124988267	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1020971	chr8:124939571-124973679	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11993947	SCHIP1	trans	lymphoblastoid	seeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:124967200-124987000	Weak transcription	Fetal Stomach	stomach
2	chr8:124970400-124971600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr8:124970600-124971600	Weak transcription	Gastric	stomach
4	chr8:124970600-124978800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr8:124970800-124972000	Enhancers	A549	lung
6	chr8:124971000-124971800	Enhancers	Stomach Mucosa	stomach

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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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