Variant report

Variant	rs6888999
Chromosome Location	chr5:147526393-147526394
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:147525612..147528709-chr5:147529097..147534248,4	MCF-7	breast:
2	chr5:147525557..147527524-chr5:147534362..147536758,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10061827	0.87[AFR][1000 genomes]
rs10065999	0.87[CEU][hapmap];0.85[CHB][hapmap]
rs10067334	0.81[CEU][hapmap];0.81[MEX][hapmap]
rs10068913	0.82[CHB][hapmap];0.83[AFR][1000 genomes]
rs10068916	0.92[ASW][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.85[LWK][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes]
rs10068988	0.85[ASW][hapmap];0.85[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.81[MEX][hapmap];0.80[TSI][hapmap]
rs10070470	0.87[AFR][1000 genomes]
rs10075227	0.87[AFR][1000 genomes]
rs11168034	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13165271	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13169394	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13360182	0.80[CEU][hapmap];0.90[CHB][hapmap]
rs1974627	0.80[AFR][1000 genomes]
rs2191680	0.85[CEU][hapmap];0.83[CHB][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes]
rs2400488	0.87[AFR][1000 genomes]
rs2400491	0.87[AFR][1000 genomes]
rs2400492	0.87[AFR][1000 genomes]
rs2400493	0.80[AFR][1000 genomes]
rs2400496	0.80[AFR][1000 genomes]
rs3935572	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4254894	0.88[CEU][hapmap];0.82[CHB][hapmap]
rs4269285	1.00[ASW][hapmap];0.85[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.88[LWK][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes]
rs4270684	0.80[AFR][1000 genomes]
rs4419576	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6872890	0.80[ASN][1000 genomes]
rs6881658	1.00[ASW][hapmap];0.85[CEU][hapmap];0.94[LWK][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap];0.81[YRI][hapmap]
rs6895745	1.00[ASW][hapmap];0.85[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.94[LWK][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap];0.81[YRI][hapmap]
rs724726	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs767569	0.80[AFR][1000 genomes]
rs767570	0.80[AFR][1000 genomes]
rs7717500	0.88[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9285669	0.82[AFR][1000 genomes]
rs9325077	0.87[AFR][1000 genomes]
rs9325078	0.87[AFR][1000 genomes]
rs9885451	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883015	chr5:147404281-147751035	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv830515	chr5:147460852-147602247	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6888999	TFF3	trans	cerebellum	SCAN
rs6888999	SPINK6	cis	Esophagus Mucosa	GTEx
rs6888999	SPINK1	cis	cerebellum	SCAN
rs6888999	FFAR2	trans	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147524000-147528200	Enhancers	Stomach Mucosa	stomach
2	chr5:147524200-147526600	Enhancers	HUVEC	blood vessel
3	chr5:147524600-147527800	Enhancers	HepG2	liver
4	chr5:147524600-147528000	Enhancers	Fetal Intestine Small	intestine
5	chr5:147525200-147526400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:147525600-147527800	Enhancers	Liver	Liver
7	chr5:147525600-147529600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr5:147526000-147526400	Enhancers	Colonic Mucosa	Colon
9	chr5:147526000-147526400	Enhancers	Hela-S3	cervix
10	chr5:147526000-147527200	Enhancers	Rectal Mucosa Donor 29	rectum
11	chr5:147526000-147527400	Enhancers	Pancreas	Pancrea
12	chr5:147526000-147527800	Enhancers	Fetal Intestine Large	intestine
13	chr5:147526000-147530000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr5:147526200-147526400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
15	chr5:147526200-147527200	Enhancers	Gastric	stomach
16	chr5:147526200-147527800	Enhancers	Sigmoid Colon	Sigmoid Colon

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