Variant report

Variant	rs2218880
Chromosome Location	chr2:152099885-152099886
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:152096040..152098295-chr2:152099658..152101934,2	MCF-7	breast:
2	chr2:152095135..152097024-chr2:152099400..152101186,2	K562	blood:

Extended variants
information (count: 96 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10169816	0.84[CHB][hapmap]
rs1040234	0.85[CEU][hapmap];1.00[YRI][hapmap]
rs1040235	0.84[CEU][hapmap];1.00[YRI][hapmap]
rs1048135	1.00[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11678123	0.82[ASN][1000 genomes]
rs11678951	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs11680338	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11683487	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11690634	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs11691055	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11691217	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11730	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.87[MEX][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12467046	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12469634	0.81[ASW][hapmap];0.85[CEU][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap]
rs12471191	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12476687	0.81[ASN][1000 genomes]
rs12624156	0.92[ASN][1000 genomes]
rs12693004	0.92[ASN][1000 genomes]
rs12987765	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12994801	0.83[AFR][1000 genomes]
rs12996459	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13001328	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs13004590	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13015862	0.80[ASN][1000 genomes]
rs13020962	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13025888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13027425	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13029661	0.83[AFR][1000 genomes]
rs1518687	0.83[AFR][1000 genomes]
rs17796622	0.81[ASW][hapmap];0.85[CEU][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs17797018	0.83[AFR][1000 genomes]
rs17798290	0.82[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2113508	0.90[ASN][1000 genomes]
rs2271811	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2278090	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2880488	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs289829	0.87[CHB][hapmap]
rs289904	0.88[EUR][1000 genomes]
rs289905	0.88[EUR][1000 genomes]
rs289906	0.90[EUR][1000 genomes]
rs289907	0.88[EUR][1000 genomes]
rs289921	0.87[EUR][1000 genomes]
rs289923	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs289924	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34028108	0.91[ASN][1000 genomes]
rs34452578	0.85[ASN][1000 genomes]
rs34538548	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs35659175	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35723696	0.82[ASN][1000 genomes]
rs35863408	0.82[ASN][1000 genomes]
rs3771882	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3771886	0.81[CHB][hapmap]
rs3771887	0.87[CHB][hapmap]
rs3771888	0.87[CHB][hapmap]
rs3854012	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3856557	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4664280	0.83[AFR][1000 genomes]
rs4664336	0.82[ASN][1000 genomes]
rs4664347	0.82[ASN][1000 genomes]
rs4664349	0.91[CHB][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.82[ASN][1000 genomes]
rs4665114	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4665137	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4665150	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4665168	0.89[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs55775354	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56335263	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs56376752	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57201382	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6433327	0.89[CEU][hapmap];0.81[GIH][hapmap]
rs66521733	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66588921	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6705511	0.80[ASW][hapmap];0.85[CEU][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap]
rs6708382	0.85[CEU][hapmap];0.81[GIH][hapmap]
rs6726634	0.82[CEU][hapmap];0.81[GIH][hapmap]
rs67303849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6739517	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6747782	0.87[CHB][hapmap]
rs6751802	0.87[CHB][hapmap]
rs6757821	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs67725431	0.92[ASN][1000 genomes]
rs67788715	0.83[AFR][1000 genomes]
rs7558169	0.82[ASN][1000 genomes]
rs7559296	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7574228	0.82[ASN][1000 genomes]
rs7587037	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7589420	0.85[CEU][hapmap]
rs9287955	0.89[CEU][hapmap];0.86[GIH][hapmap]
rs9287956	0.88[CEU][hapmap]
rs958525	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523849	chr2:151718133-152143524	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	esv3693426	chr2:151725792-152295862	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv834417	chr2:151980473-152154950	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1014936	chr2:152019809-152118479	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1012891	chr2:152019809-152306897	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv1013484	chr2:152028515-152473913	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv535983	chr2:152028515-152473913	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2218880	TNFAIP6	cis	parietal	SCAN
rs2218880	NMI	Cis_1M	lymphoblastoid	RTeQTL
rs2218880	TNFAIP6	cis	Muscle Skeletal	GTEx
rs2218880	TNFAIP6	cis	Whole Blood	GTEx
rs2218880	RBM43	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152092600-152103000	Weak transcription	Ovary	ovary
2	chr2:152093000-152105200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr2:152094400-152105000	Weak transcription	Adipose Nuclei	Adipose
4	chr2:152094400-152105000	Weak transcription	Liver	Liver
5	chr2:152094400-152105200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:152094400-152117000	Weak transcription	A549	lung
7	chr2:152095200-152105200	Weak transcription	Osteobl	bone
8	chr2:152095400-152105200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr2:152095400-152107200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr2:152095600-152105200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr2:152096000-152104400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:152096000-152105200	Weak transcription	NHDF-Ad	bronchial
13	chr2:152098400-152105000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr2:152098400-152105400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:152098800-152105400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr2:152099800-152100000	Enhancers	Placenta Amnion	Placenta Amnion

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