Variant report

Variant	rs2602880
Chromosome Location	chr4:100040653-100040654
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 94 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10017466	0.88[CEU][hapmap]
rs1042364	0.96[CEU][hapmap]
rs1042365	0.96[CEU][hapmap]
rs1126670	0.88[CEU][hapmap]
rs1126671	0.88[CEU][hapmap]
rs1126672	0.96[CEU][hapmap]
rs1126673	0.88[CEU][hapmap]
rs1154400	0.81[CEU][hapmap]
rs1154405	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs1154410	0.96[CEU][hapmap];1.00[YRI][hapmap]
rs1230154	0.87[CEU][hapmap]
rs13110176	0.96[CEU][hapmap]
rs13110764	0.96[CEU][hapmap]
rs13112176	0.96[CEU][hapmap]
rs13113166	0.88[CEU][hapmap]
rs1311615	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs1311616	0.96[CEU][hapmap];1.00[YRI][hapmap]
rs1311617	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs1311618	0.87[CEU][hapmap];1.00[YRI][hapmap]
rs1311620	0.81[CEU][hapmap]
rs13125919	0.82[YRI][hapmap]
rs13129488	0.96[CEU][hapmap]
rs13133647	0.96[CEU][hapmap]
rs13138294	0.96[CEU][hapmap]
rs13143133	0.96[CEU][hapmap]
rs13145727	0.83[YRI][hapmap]
rs1377689	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs1453874	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs17217949	0.96[CEU][hapmap]
rs17218003	0.96[CEU][hapmap]
rs17218073	0.96[CEU][hapmap]
rs17218108	0.96[CEU][hapmap]
rs17218141	0.96[CEU][hapmap]
rs17218162	0.96[CEU][hapmap]
rs17218239	0.96[CEU][hapmap]
rs17218288	0.96[CEU][hapmap]
rs17218560	0.96[CEU][hapmap]
rs17218602	0.96[CEU][hapmap]
rs17817359	0.96[CEU][hapmap]
rs17817868	0.96[CEU][hapmap]
rs17817958	0.96[CEU][hapmap]
rs1803037	0.82[YRI][hapmap]
rs1984362	0.92[CEU][hapmap]
rs1984364	0.92[CEU][hapmap]
rs2602847	1.00[YRI][hapmap]
rs2602863	0.85[EUR][1000 genomes]
rs2602864	0.81[AMR][1000 genomes]
rs2602881	0.80[EUR][1000 genomes]
rs2602882	0.81[EUR][1000 genomes]
rs2602883	0.80[EUR][1000 genomes]
rs2602895	0.96[CEU][hapmap]
rs2602896	0.96[CEU][hapmap]
rs2851246	0.96[CEU][hapmap]
rs2851247	0.96[CEU][hapmap]
rs2851248	0.96[CEU][hapmap]
rs2851250	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2851254	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2851258	0.80[AMR][1000 genomes]
rs2851261	0.84[AMR][1000 genomes]
rs2851272	0.82[AMR][1000 genomes]
rs2851277	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs2851278	1.00[CEU][hapmap]
rs2851280	0.80[AMR][1000 genomes]
rs29001203	0.96[CEU][hapmap]
rs29001217	0.85[AMR][1000 genomes]
rs3018047	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs3018048	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs34936974	0.96[CEU][hapmap]
rs3919370	0.92[CEU][hapmap]
rs4699712	0.96[CEU][hapmap]
rs4699713	0.96[CEU][hapmap]
rs4699714	0.96[CEU][hapmap]
rs4699716	0.87[CEU][hapmap]
rs4699717	0.91[CEU][hapmap]
rs6532782	0.81[AMR][1000 genomes]
rs6532798	0.88[CEU][hapmap]
rs6837685	0.88[CEU][hapmap]
rs7375618	0.81[AMR][1000 genomes]
rs7434491	0.92[CEU][hapmap]
rs7669636	0.96[CEU][hapmap]
rs7670060	0.96[CEU][hapmap]
rs7670241	0.96[CEU][hapmap]
rs7670638	0.91[CEU][hapmap]
rs7684986	0.82[YRI][hapmap]
rs7689753	0.86[CEU][hapmap]
rs7694646	0.95[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009017	chr4:99669441-100406394	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1002927	chr4:99952472-100148690	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv879656	chr4:99976646-100533722	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1005446	chr4:99988287-100121669	Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv537196	chr4:99988287-100121669	Strong transcription ZNF genes & repeats Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv1002574	chr4:100023999-100133693	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv3528915	chr4:100025155-100096234	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv3528916	chr4:100025155-100096234	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2602880	ADH5	cis	Whole Blood	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100012800-100063800	Weak transcription	Aorta	Aorta
2	chr4:100021000-100041200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:100023000-100055600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:100035000-100098200	Weak transcription	Ovary	ovary
5	chr4:100038800-100055200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr4:100039400-100042000	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr4:100039600-100041200	Enhancers	Duodenum Mucosa	Duodenum
8	chr4:100039800-100064800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr4:100040000-100043800	Weak transcription	Fetal Lung	lung
10	chr4:100040000-100045000	Weak transcription	Liver	Liver
11	chr4:100040000-100050800	Weak transcription	Fetal Intestine Large	intestine
12	chr4:100040400-100040800	Weak transcription	HepG2	liver

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