Variant report

Variant	rs6984540
Chromosome Location	chr8:90847952-90847953
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:153928343..153930810-chr8:90845808..90848291,2	MCF-7	breast:
2	chr8:90844734..90847246-chr8:90847760..90849982,2	MCF-7	breast:
3	chr8:90842015..90844808-chr8:90846350..90848041,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160741	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10094579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10096271	0.93[ASN][1000 genomes]
rs11785163	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11989430	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12155807	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12675822	0.84[YRI][hapmap];0.83[AFR][1000 genomes]
rs12680009	0.90[YRI][hapmap];0.83[AFR][1000 genomes]
rs13260987	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13278954	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13280951	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16900888	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs16901016	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2189025	0.91[EUR][1000 genomes]
rs2338882	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2338883	0.94[CHB][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs28405481	0.97[EUR][1000 genomes]
rs28461337	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28528187	0.86[EUR][1000 genomes]
rs28766093	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2879287	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs34525502	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34642426	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34699769	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34970073	0.97[EUR][1000 genomes]
rs35183880	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs39771	0.81[ASN][1000 genomes]
rs426240	0.81[ASN][1000 genomes]
rs62530862	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62530908	0.98[EUR][1000 genomes]
rs7013987	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs7015630	1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[YRI][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	nsv520356	chr8:90823687-90857989	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv2761448	chr8:90837630-90853986	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6984540	RIPK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:90839200-90848400	Weak transcription	Osteobl	bone
2	chr8:90845800-90848000	Flanking Active TSS	GM12878-XiMat	blood
3	chr8:90845800-90850200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr8:90846000-90850400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr8:90846000-90850600	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr8:90846200-90848000	Enhancers	Primary hematopoietic stem cells	blood
7	chr8:90846200-90848200	Weak transcription	NHLF	lung
8	chr8:90846200-90848600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr8:90846600-90850000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr8:90846800-90848600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr8:90847200-90848600	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr8:90847200-90848600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr8:90847200-90849000	Enhancers	HUVEC	blood vessel
14	chr8:90847200-90849000	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr8:90847200-90849000	Enhancers	NHDF-Ad	bronchial
16	chr8:90847200-90849800	Enhancers	Primary B cells from peripheral blood	blood
17	chr8:90847200-90850200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr8:90847400-90848400	Weak transcription	Primary T cells from cord blood	blood
19	chr8:90847400-90849200	Enhancers	A549	lung
20	chr8:90847600-90848000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr8:90847600-90848400	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr8:90847600-90848600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr8:90847600-90849000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr8:90847600-90849000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr8:90847600-90850000	Enhancers	Stomach Mucosa	stomach
26	chr8:90847600-90860600	Weak transcription	Aorta	Aorta
27	chr8:90847800-90848200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr8:90847800-90848400	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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