Variant report

Variant	rs398957
Chromosome Location	chr8:90869980-90869981
allele	C/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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:90869811..90872309-chr8:90877173..90879191,2	MCF-7	breast:
2	chr8:90867270..90880457-chr8:90913050..90918593,18	MCF-7	breast:
3	chr8:90864006..90868898-chr8:90869518..90873802,5	K562	blood:
4	chr8:90869160..90871090-chr8:90871381..90873801,2	MCF-7	breast:
5	chr8:90869094..90872518-chr8:90873810..90876034,4	MCF-7	breast:
6	chr8:90864006..90868898-chr8:90869518..90873896,4	K562	blood:
7	chr8:90868769..90874649-chr8:90891359..90894975,5	MCF-7	breast:
8	chr8:90866711..90872793-chr8:90887380..90891820,9	MCF-7	breast:
9	chr8:90737773..90739680-chr8:90867503..90870182,2	MCF-7	breast:
10	chr8:90858582..90866507-chr8:90866541..90873248,10	MCF-7	breast:
11	chr8:90866902..90871267-chr8:90912071..90916231,7	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000207359	Chromatin interaction
ENSG00000164823	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11782542	0.82[CHB][hapmap]
rs379174	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs381326	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs381948	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs393781	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs39517	0.85[CEU][hapmap];0.91[ASN][1000 genomes]
rs39518	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs39770	1.00[JPT][hapmap]
rs400077	1.00[JPT][hapmap]
rs400613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40383	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs404146	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs404292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs410014	0.92[CEU][hapmap];0.82[CHB][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs410927	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs428441	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs431623	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]
rs431985	0.92[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs454020	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[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
rs398957	RIPK2	cis	parietal	SCAN
rs398957	MMP16	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:90861000-90870200	Weak transcription	HMEC	breast
2	chr8:90861000-90871000	Weak transcription	Right Atrium	heart
3	chr8:90861800-90870200	Weak transcription	Brain Hippocampus Middle	brain
4	chr8:90864800-90870400	Weak transcription	Aorta	Aorta
5	chr8:90866600-90873400	Enhancers	HSMMtube	muscle
6	chr8:90867000-90870400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr8:90867600-90871200	Enhancers	Fetal Muscle Leg	muscle
8	chr8:90867800-90870200	Enhancers	A549	lung
9	chr8:90868200-90871200	Enhancers	Muscle Satellite Cultured Cells	--
10	chr8:90868200-90872000	Enhancers	HSMM	muscle
11	chr8:90868400-90870200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr8:90868600-90870200	Weak transcription	Colon Smooth Muscle	Colon
13	chr8:90868800-90871200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr8:90869000-90872000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr8:90869200-90870200	Weak transcription	Pancreas	Pancrea
16	chr8:90869200-90870400	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr8:90869200-90871200	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr8:90869200-90873800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr8:90869600-90870000	Enhancers	Brain Cingulate Gyrus	brain
20	chr8:90869600-90870000	Weak transcription	Ovary	ovary
21	chr8:90869600-90870200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr8:90869600-90870200	Weak transcription	Placenta	Placenta
23	chr8:90869600-90870800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr8:90869600-90871600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr8:90869600-90872400	Enhancers	Adipose Nuclei	Adipose
26	chr8:90869800-90870600	Enhancers	Osteobl	bone
27	chr8:90869800-90871000	Weak transcription	Brain Anterior Caudate	brain
28	chr8:90869800-90871600	Enhancers	Brain Substantia Nigra	brain
29	chr8:90869800-90872400	Enhancers	Rectal Smooth Muscle	rectum

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