Variant report

Variant	rs2169554
Chromosome Location	chr3:100319914-100319915
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10428254	0.94[ASN][1000 genomes]
rs10511187	0.95[ASN][1000 genomes]
rs10511188	0.95[ASN][1000 genomes]
rs10936264	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1165521	0.89[ASN][1000 genomes]
rs11923487	0.83[ASN][1000 genomes]
rs12634935	0.95[ASN][1000 genomes]
rs12635503	0.95[ASN][1000 genomes]
rs12636790	0.95[ASN][1000 genomes]
rs12637319	0.95[ASN][1000 genomes]
rs1305373	0.95[ASN][1000 genomes]
rs1305375	0.95[ASN][1000 genomes]
rs13069547	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13321761	0.95[ASN][1000 genomes]
rs1842732	0.93[ASN][1000 genomes]
rs4129205	0.83[ASN][1000 genomes]
rs57404153	0.83[ASN][1000 genomes]
rs58618663	0.85[ASN][1000 genomes]
rs60151360	0.94[ASN][1000 genomes]
rs61549238	0.87[ASN][1000 genomes]
rs619149	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs653530	0.95[ASN][1000 genomes]
rs661266	0.95[ASN][1000 genomes]
rs6763638	0.83[ASN][1000 genomes]
rs6768258	0.95[ASN][1000 genomes]
rs6770693	0.95[ASN][1000 genomes]
rs6771421	0.95[ASN][1000 genomes]
rs6773148	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6783630	0.95[ASN][1000 genomes]
rs6785969	0.95[ASN][1000 genomes]
rs6786853	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73141183	0.88[ASN][1000 genomes]
rs7426414	0.88[ASN][1000 genomes]
rs7426462	0.83[ASN][1000 genomes]
rs7427360	0.83[ASN][1000 genomes]
rs7432710	0.83[ASN][1000 genomes]
rs7433875	0.83[ASN][1000 genomes]
rs7617909	0.83[ASN][1000 genomes]
rs9290097	0.94[ASN][1000 genomes]
rs9290098	0.95[ASN][1000 genomes]
rs9290099	0.95[ASN][1000 genomes]
rs9290100	0.95[ASN][1000 genomes]
rs9790050	0.95[ASN][1000 genomes]
rs9790137	0.95[ASN][1000 genomes]
rs9790219	0.95[ASN][1000 genomes]
rs9818800	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9825818	0.83[ASN][1000 genomes]
rs9829641	0.94[ASN][1000 genomes]
rs9829972	0.93[ASN][1000 genomes]
rs9834474	0.94[ASN][1000 genomes]
rs9834776	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9838918	0.94[ASN][1000 genomes]
rs9853434	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9856061	0.94[ASN][1000 genomes]
rs9856338	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9860005	0.95[ASN][1000 genomes]
rs9874401	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751965	chr3:100299310-100462527	Enhancers Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	esv2751966	chr3:100299310-100468500	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	esv2756284	chr3:100299329-100427937	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv2752830	chr3:100299329-100442478	Enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv432464	chr3:100299329-100442478	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	esv2751967	chr3:100299329-100455139	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	esv2751968	chr3:100299329-100476713	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv432466	chr3:100299329-100476713	Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv536667	chr3:100308355-100445857	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv460770	chr3:100310812-100433592	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv591150	chr3:100310812-100433592	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	esv2751969	chr3:100312499-100479384	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
13	esv2763708	chr3:100317928-100442509	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2169554	TMEM45A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100318200-100324200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:100318600-100320600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr3:100318800-100323200	Enhancers	HMEC	breast
4	chr3:100319000-100320000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr3:100319000-100320600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:100319000-100323000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:100319200-100320000	Enhancers	Esophagus	oesophagus
8	chr3:100319200-100321200	Enhancers	HepG2	liver
9	chr3:100319200-100321600	Enhancers	Duodenum Mucosa	Duodenum
10	chr3:100319400-100321400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr3:100319400-100321400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr3:100319400-100322000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr3:100319400-100322200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr3:100319600-100320200	Flanking Active TSS	NHEK	skin
15	chr3:100319600-100320400	ZNF genes & repeats	Fetal Intestine Small	intestine
16	chr3:100319600-100321400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr3:100319600-100321600	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr3:100319600-100321800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr3:100319600-100322000	Weak transcription	Primary T cells from cord blood	blood
20	chr3:100319600-100322000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr3:100319600-100322000	Weak transcription	Thymus	Thymus
22	chr3:100319800-100320800	Enhancers	Dnd41	blood
23	chr3:100319800-100321200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr3:100319800-100321800	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr3:100319800-100322000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr3:100319800-100322200	Weak transcription	Fetal Thymus	thymus
27	chr3:100319800-100322800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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