Variant report

Variant	rs28502265
Chromosome Location	chr2:20130145-20130146
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:20123825..20126159-chr2:20127978..20130172,2	K562	blood:
2	chr2:20128853..20131612-chr2:20133463..20134985,2	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10169398	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10175095	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10197385	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10208878	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10495701	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1060742	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11096632	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11888045	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11889206	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12052274	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12613209	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12617761	0.81[ASN][1000 genomes]
rs12620863	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13415707	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13421472	0.81[ASN][1000 genomes]
rs1381817	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16987265	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2293671	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28477921	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35957485	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62109397	0.81[ASN][1000 genomes]
rs62109398	0.81[ASN][1000 genomes]
rs62109399	0.81[ASN][1000 genomes]
rs62109404	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62109406	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62109413	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62109415	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62109416	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62109418	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62109419	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62109420	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62109421	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6707471	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6719397	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6755153	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7563410	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7572167	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7589478	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7594214	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[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	nsv873712	chr2:19955245-20131079	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
2	nsv873713	chr2:19955245-20144372	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
3	nsv873715	chr2:20059323-20144372	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
4	nsv521619	chr2:20098208-20150817	Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	nsv527453	chr2:20109061-20160209	ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs28502265	TTC32	cis	Heart Left Ventricle	GTEx
rs28502265	TTC32	cis	Adipose Subcutaneous	GTEx
rs28502265	TTC32	cis	Esophagus Muscularis	GTEx
rs28502265	TTC32	cis	multi-tissue	Pritchard
rs28502265	TTC32	cis	Thyroid	GTEx
rs28502265	TTC32	cis	Esophagus Mucosa	GTEx
rs28502265	TTC32	Cis_1M	lymphoblastoid	RTeQTL
rs28502265	TTC32	cis	Stomach	GTEx
rs28502265	TTC32	cis	lung	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20102800-20173200	Weak transcription	Fetal Brain Male	brain
2	chr2:20105400-20130200	Weak transcription	Lung	lung
3	chr2:20108800-20137400	Weak transcription	Right Ventricle	heart
4	chr2:20114400-20143800	Weak transcription	Brain Substantia Nigra	brain
5	chr2:20117600-20188400	Weak transcription	Brain Angular Gyrus	brain
6	chr2:20121600-20130600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr2:20121600-20135800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr2:20122800-20130600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr2:20123400-20135800	Weak transcription	Brain Hippocampus Middle	brain
10	chr2:20124400-20130600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr2:20124800-20142800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr2:20125200-20132800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr2:20125400-20132800	Weak transcription	Gastric	stomach
14	chr2:20126200-20130400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr2:20126200-20130600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:20126400-20137200	Weak transcription	Colonic Mucosa	Colon
17	chr2:20126600-20130400	ZNF genes & repeats	Adipose Nuclei	Adipose
18	chr2:20126600-20130600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
19	chr2:20126800-20130400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
20	chr2:20126800-20130600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
21	chr2:20126800-20131200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr2:20127000-20130400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
23	chr2:20127000-20130400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
24	chr2:20127200-20130600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr2:20127200-20132200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr2:20127200-20132800	Weak transcription	NH-A	brain
27	chr2:20127400-20130400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
28	chr2:20127400-20130600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:20127400-20130600	Strong transcription	Ovary	ovary
30	chr2:20127400-20132200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr2:20127400-20167800	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr2:20127600-20139200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr2:20127800-20135800	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr2:20128000-20130400	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr2:20128000-20130600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr2:20128000-20130600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr2:20128000-20131200	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr2:20128000-20137400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr2:20128000-20139200	Weak transcription	Pancreas	Pancrea
40	chr2:20128200-20132600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr2:20128400-20130600	Strong transcription	NHDF-Ad	bronchial
42	chr2:20128400-20130800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:20128400-20131800	Strong transcription	HSMM	muscle
44	chr2:20128400-20188400	Weak transcription	Colon Smooth Muscle	Colon
45	chr2:20128400-20189200	Weak transcription	Small Intestine	intestine
46	chr2:20128600-20130200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr2:20128600-20130400	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
48	chr2:20128600-20130600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr2:20128600-20130600	Strong transcription	Thymus	Thymus
50	chr2:20128600-20131000	Strong transcription	H1 Cell Line	embryonic stem cell

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