Variant report

Variant	rs3742370
Chromosome Location	chr14:35745642-35745643
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr14:35745620-35745709	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:35744140..35746636-chr14:35750906..35752624,2	K562	blood:
2	chr14:35742696..35750735-chr14:35870363..35874138,7	MCF-7	breast:
3	chr14:35737913..35740720-chr14:35744173..35747290,3	K562	blood:
4	chr14:35737913..35739770-chr14:35744109..35746101,2	K562	blood:
5	chr14:35734999..35737663-chr14:35744257..35745770,2	MCF-7	breast:
6	chr14:35745539..35747078-chr14:35765050..35766913,2	K562	blood:

No data

Variant related genes	Relation type
PSMA6	TF binding region
ENSG00000100906	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10129963	0.81[CHD][hapmap]
rs10134834	0.89[ASN][1000 genomes]
rs11156876	0.88[ASN][1000 genomes]
rs11621075	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12433113	0.86[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs12587689	0.80[ASN][1000 genomes]
rs12878391	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17512585	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1884716	0.89[ASN][1000 genomes]
rs1951273	0.85[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap]
rs1957107	0.81[CEU][hapmap]
rs2415276	0.91[ASN][1000 genomes]
rs2415277	0.91[ASN][1000 genomes]
rs2415279	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2415286	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28525079	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2899831	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];0.93[ASN][1000 genomes]
rs34031432	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35992180	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4530028	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4981273	0.87[ASN][1000 genomes]
rs6571710	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7143346	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];0.96[LWK][hapmap];0.97[MKK][hapmap];0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7157492	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7157736	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7158402	0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs8003136	0.93[CHB][hapmap];0.92[CHD][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs8004740	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs8005078	1.00[ASW][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.84[JPT][hapmap];0.96[LWK][hapmap];0.91[ASN][1000 genomes]
rs8008319	0.93[CHB][hapmap];0.84[JPT][hapmap];0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs8009707	0.81[CEU][hapmap]
rs8015175	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs8181982	0.90[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[LWK][hapmap];0.97[MKK][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949617	chr14:35379923-35825436	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS 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 target site	73 gene(s)	inside rSNPs	diseases
2	nsv1043470	chr14:35398522-35754029	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv542031	chr14:35398522-35754029	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
4	nsv870305	chr14:35488290-35852349	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv1044515	chr14:35510785-35756317	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv1053604	chr14:35548276-35825805	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	nsv1052392	chr14:35563220-35893309	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	diseases
8	nsv542036	chr14:35563220-35893309	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	diseases
9	nsv1038396	chr14:35714499-35788189	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv1045288	chr14:35735886-35788189	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv1043840	chr14:35739319-35791879	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3742370	NKX2-1	cis	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:35684600-35760800	Weak transcription	HSMM	muscle
2	chr14:35705400-35749800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr14:35706800-35760800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr14:35709800-35753600	Weak transcription	Small Intestine	intestine
5	chr14:35716800-35760600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr14:35716800-35761000	Weak transcription	Spleen	Spleen
7	chr14:35717000-35760800	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr14:35717600-35753800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr14:35722000-35754000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr14:35722000-35760800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr14:35724200-35756400	Weak transcription	Left Ventricle	heart
12	chr14:35727200-35754600	Weak transcription	NHDF-Ad	bronchial
13	chr14:35727200-35756400	Weak transcription	Stomach Mucosa	stomach
14	chr14:35727200-35761000	Weak transcription	NHLF	lung
15	chr14:35727400-35754000	Weak transcription	HUVEC	blood vessel
16	chr14:35728000-35750200	Weak transcription	Ovary	ovary
17	chr14:35728400-35748400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr14:35728400-35754600	Weak transcription	K562	blood
19	chr14:35728400-35755000	Weak transcription	Colonic Mucosa	Colon
20	chr14:35730000-35747200	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr14:35730000-35751000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr14:35730200-35760600	Weak transcription	Fetal Brain Female	brain
23	chr14:35730400-35747000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr14:35730400-35753400	Weak transcription	Primary B cells from peripheral blood	blood
25	chr14:35731800-35756000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr14:35733400-35747200	Weak transcription	HSMMtube	muscle
27	chr14:35734400-35760600	Weak transcription	Right Ventricle	heart
28	chr14:35734400-35760800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr14:35734600-35749400	Weak transcription	Fetal Kidney	kidney
30	chr14:35734600-35750400	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr14:35734600-35752400	Weak transcription	NH-A	brain
32	chr14:35735600-35745800	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr14:35735600-35747400	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr14:35735800-35745800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr14:35735800-35746600	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr14:35735800-35748000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr14:35736000-35746400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr14:35736000-35760800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr14:35736600-35754000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr14:35737400-35761000	Weak transcription	Gastric	stomach
41	chr14:35737600-35751800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr14:35738600-35750200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr14:35738800-35759400	Weak transcription	Placenta	Placenta
44	chr14:35739000-35746000	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr14:35739000-35746600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr14:35739200-35745800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr14:35739800-35746200	Weak transcription	Pancreas	Pancrea
48	chr14:35740000-35753600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr14:35740000-35754800	Weak transcription	Adipose Nuclei	Adipose
50	chr14:35740000-35756600	Weak transcription	NHEK	skin

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