Variant report

Variant	rs431623
Chromosome Location	chr8:90865461-90865462
allele	A/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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:90859420..90866965-chr8:90912674..90917180,23	MCF-7	breast:
2	chr8:90858582..90866507-chr8:90866541..90873248,10	MCF-7	breast:
3	chr8:90861478..90863438-chr8:90864534..90866909,2	MCF-7	breast:
4	chr8:90864006..90868898-chr8:90869518..90873896,4	K562	blood:
5	chr8:90864006..90868898-chr8:90869518..90873802,5	K562	blood:
6	chr8:90860679..90862898-chr8:90864045..90867127,3	K562	blood:
7	chr8:90856651..90860319-chr8:90861646..90865925,3	K562	blood:
8	chr8:90855177..90868995-chr8:90994125..91001070,26	MCF-7	breast:
9	chr8:90854658..90857066-chr8:90864684..90867899,3	MCF-7	breast:
10	chr8:90862840..90866421-chr8:90892520..90896963,6	MCF-7	breast:

No data

No data

No data

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11782542	0.82[CHB][hapmap]
rs379174	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs381326	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs381948	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs393781	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs39517	0.89[CEU][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs39518	0.85[ASN][1000 genomes]
rs398957	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs400613	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs40383	0.88[CEU][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs404146	1.00[ASN][1000 genomes]
rs404292	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs410014	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs410927	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs428441	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs431985	0.96[CEU][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs454020	0.92[CEU][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933502	chr8:90702392-91049100	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
2	nsv934114	chr8:90720182-90999106	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
3	nsv891182	chr8:90785685-90888786	Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs431623	RIPK2	cis	parietal	SCAN
rs431623	MMP16	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:90861000-90866600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr8:90861000-90868400	Weak transcription	Ovary	ovary
3	chr8:90861000-90870200	Weak transcription	HMEC	breast
4	chr8:90861000-90871000	Weak transcription	Right Atrium	heart
5	chr8:90861200-90869600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr8:90861200-90869800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr8:90861400-90869000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr8:90861600-90868200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr8:90861600-90868200	Weak transcription	HSMM	muscle
10	chr8:90861800-90869200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr8:90861800-90869200	Weak transcription	Brain Anterior Caudate	brain
12	chr8:90861800-90870200	Weak transcription	Brain Hippocampus Middle	brain
13	chr8:90864800-90870400	Weak transcription	Aorta	Aorta
14	chr8:90865400-90867400	Enhancers	A549	lung

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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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