Variant report

Variant	rs454561
Chromosome Location	chr8:90836615-90836616
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr8:90836359-90837183	H1-hESC	embryonic stem cell:	n/a	n/a
2	SIN3A	chr8:90836539-90837118	H1-hESC	embryonic stem cell:	n/a	n/a
3	TEAD4	chr8:90836401-90836789	H1-hESC	embryonic stem cell:	n/a	n/a
4	TBP	chr8:90836584-90836670	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:90824515..90827081-chr8:90836313..90840458,3	MCF-7	breast:

Variant related genes	Relation type
COX6B1P6	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1003843	0.81[CHB][hapmap]
rs10112852	0.82[CHB][hapmap]
rs13280951	0.85[ASN][1000 genomes]
rs218907	0.82[CHB][hapmap]
rs218908	0.82[CHB][hapmap]
rs218913	0.81[CHB][hapmap]
rs218929	0.81[CHB][hapmap]
rs2338882	0.85[ASN][1000 genomes]
rs28144	0.82[AFR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28461337	0.85[ASN][1000 genomes]
rs2975240	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs368812	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs369771	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs370282	0.92[EUR][1000 genomes]
rs374957	0.89[JPT][hapmap]
rs376110	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs386857	0.89[JPT][hapmap]
rs394108	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs39515	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs39516	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs39519	0.89[JPT][hapmap];0.87[YRI][hapmap]
rs39767	0.91[EUR][1000 genomes]
rs39768	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs39769	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs39771	0.89[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes]
rs400571	0.89[JPT][hapmap]
rs402434	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs40381	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs40382	0.94[EUR][1000 genomes]
rs40457	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40458	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40547	0.92[EUR][1000 genomes]
rs40636	0.92[EUR][1000 genomes]
rs40637	0.82[AFR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40638	0.92[EUR][1000 genomes]
rs40639	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs410577	0.89[JPT][hapmap]
rs421411	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs422559	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs42345	0.80[AFR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs42346	0.92[EUR][1000 genomes]
rs43135	0.94[EUR][1000 genomes]
rs43136	0.89[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs43226	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs43227	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs43228	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs43229	0.89[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes]
rs438485	0.89[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs441548	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs445172	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs445675	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs447611	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs452694	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs453266	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62530862	0.86[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	nsv968495	chr8:90835687-90842298	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs454561	RP11-37B2.1	cis	Adipose Subcutaneous	GTEx
rs454561	RIPK2	Cis_1M	lymphoblastoid	RTeQTL
rs454561	RP11-37B2.1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:90828000-90845800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr8:90836400-90837000	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr8:90836400-90837000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr8:90836400-90837200	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr8:90836400-90837200	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr8:90836400-90837200	Enhancers	Placenta Amnion	Placenta Amnion
7	chr8:90836400-90837800	Enhancers	Fetal Intestine Large	intestine
8	chr8:90836600-90837000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
9	chr8:90836600-90837000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr8:90836600-90837000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr8:90836600-90837000	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr8:90836600-90837000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr8:90836600-90837000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr8:90836600-90837000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr8:90836600-90837200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr8:90836600-90837200	Enhancers	H1 Cell Line	embryonic stem cell
17	chr8:90836600-90837200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr8:90836600-90837200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr8:90836600-90837200	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr8:90836600-90837200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr8:90836600-90837200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr8:90836600-90837400	Enhancers	Fetal Intestine Small	intestine
23	chr8:90836600-90837400	Flanking Active TSS	HepG2	liver
24	chr8:90836600-90837600	Enhancers	Stomach Mucosa	stomach

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