Variant report

Variant	rs62109406
Chromosome Location	chr2:20115111-20115112
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20100249..20101997-chr2:20113372..20115180,2	MCF-7	breast:
2	chr2:20110363..20112943-chr2:20112960..20116017,3	K562	blood:
3	chr2:20100607..20103540-chr2:20114213..20116931,4	K562	blood:

Variant related genes	Relation type
ENSG00000271991	Chromatin interaction
ENSG00000183891	Chromatin interaction

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];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10175095	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10197385	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10208878	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10495701	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1060742	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11096632	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11888045	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11889206	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12052274	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12613209	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12617761	0.81[ASN][1000 genomes]
rs12620863	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13415707	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13421472	0.81[ASN][1000 genomes]
rs1381817	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16987265	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2293671	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28477921	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28502265	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35957485	0.95[AMR][1000 genomes];0.97[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	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62109413	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62109415	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62109416	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62109418	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62109419	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62109420	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62109421	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6707471	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6719397	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6755153	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7563410	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7572167	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7589478	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7594214	1.00[AMR][1000 genomes];0.99[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
rs62109406	TTC32	cis	multi-tissue	Pritchard
rs62109406	TTC32	cis	Thyroid	GTEx
rs62109406	TTC32	cis	Adipose Subcutaneous	GTEx
rs62109406	TTC32	cis	Heart Left Ventricle	GTEx
rs62109406	TTC32	cis	Esophagus Muscularis	GTEx
rs62109406	TTC32	cis	Stomach	GTEx
rs62109406	TTC32	cis	Esophagus Mucosa	GTEx
rs62109406	TTC32	Cis_1M	lymphoblastoid	RTeQTL
rs62109406	TTC32	cis	lung	GTEx

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20102200-20116000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:20102400-20126600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:20102600-20115800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr2:20102600-20115800	Weak transcription	Fetal Stomach	stomach
5	chr2:20102600-20119000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr2:20102600-20127600	Weak transcription	Fetal Muscle Leg	muscle
7	chr2:20102600-20127800	Weak transcription	Aorta	Aorta
8	chr2:20102600-20128000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr2:20102800-20115600	Weak transcription	Fetal Intestine Small	intestine
10	chr2:20102800-20115800	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr2:20102800-20116000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr2:20102800-20123200	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr2:20102800-20123600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr2:20102800-20126600	Weak transcription	Adipose Nuclei	Adipose
15	chr2:20102800-20126600	Weak transcription	Fetal Lung	lung
16	chr2:20102800-20126800	Weak transcription	Fetal Kidney	kidney
17	chr2:20102800-20127200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:20102800-20127600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr2:20102800-20127600	Weak transcription	Stomach Smooth Muscle	stomach
20	chr2:20102800-20128800	Weak transcription	Liver	Liver
21	chr2:20102800-20128800	Weak transcription	Brain Germinal Matrix	brain
22	chr2:20102800-20129000	Weak transcription	Brain Anterior Caudate	brain
23	chr2:20102800-20173200	Weak transcription	Fetal Brain Male	brain
24	chr2:20103000-20116200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr2:20103000-20126800	Weak transcription	Primary hematopoietic stem cells	blood
26	chr2:20103000-20127400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr2:20105000-20127400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr2:20105400-20129000	Weak transcription	Primary T cells from cord blood	blood
29	chr2:20105400-20130200	Weak transcription	Lung	lung
30	chr2:20106600-20117400	Weak transcription	GM12878-XiMat	blood
31	chr2:20107800-20123400	Weak transcription	Left Ventricle	heart
32	chr2:20108600-20127400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr2:20108800-20137400	Weak transcription	Right Ventricle	heart
34	chr2:20109200-20126600	Weak transcription	Primary B cells from cord blood	blood
35	chr2:20110800-20117600	Weak transcription	Pancreas	Pancrea
36	chr2:20111000-20126600	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr2:20111800-20115800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr2:20111800-20116200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr2:20111800-20127800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr2:20112000-20115600	Weak transcription	Ovary	ovary
41	chr2:20112200-20115800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr2:20112200-20116000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr2:20112200-20128400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr2:20112200-20130000	Weak transcription	HSMMtube	muscle
45	chr2:20112400-20116000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr2:20112400-20116000	Weak transcription	HSMM	muscle
47	chr2:20112400-20123200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr2:20112400-20126600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr2:20112400-20126800	Weak transcription	Duodenum Mucosa	Duodenum
50	chr2:20112400-20128000	Weak transcription	Osteobl	bone

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