Variant report

Variant	rs7246435
Chromosome Location	chr19:53743134-53743135
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10403807	0.89[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10404561	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10407257	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10412650	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10419020	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10419211	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10419777	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10419854	0.83[ASN][1000 genomes]
rs10424137	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28434722	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28658052	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28676766	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28683678	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4411615	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45575234	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56121768	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61576844	0.81[EUR][1000 genomes]
rs6509740	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7245436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7249238	1.00[ASN][1000 genomes]
rs7250202	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7253386	1.00[ASN][1000 genomes]
rs7260260	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7260595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8100275	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8100627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8107688	0.84[CEU][hapmap];0.91[GIH][hapmap];0.85[EUR][1000 genomes]
rs8107870	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065143	chr19:53507142-53853363	Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv544063	chr19:53507142-53853363	ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv1058019	chr19:53507142-53904508	ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
4	nsv544064	chr19:53507142-53904508	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv912342	chr19:53581151-54010759	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv1063630	chr19:53591444-54419183	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	282 gene(s)	inside rSNPs	diseases
7	nsv1055378	chr19:53603268-53951855	Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
8	nsv544065	chr19:53603268-53951855	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
9	esv2830362	chr19:53681132-53933147	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv1064604	chr19:53730688-53751243	ZNF genes & repeats Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv580079	chr19:53732590-53756120	ZNF genes & repeats Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv1055236	chr19:53739483-53778339	Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7246435	LENG1	cis	Liver	GTEx
rs7246435	NDUFA10	cis	Liver	GTEx
rs7246435	ISOC2	cis	cerebellum	SCAN
rs7246435	HSS00006891	cis	multi-tissue	Pritchard
rs7246435	EPN1	cis	parietal	SCAN
rs7246435	SHISA7	cis	parietal	SCAN
rs7246435	LENG1	cis	multi-tissue	Pritchard
rs7246435	NDUFA10	trans	multi-tissue	Pritchard

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53728200-53748800	ZNF genes & repeats	Liver	Liver
2	chr19:53733600-53755200	ZNF genes & repeats	Adipose Nuclei	Adipose
3	chr19:53733600-53755800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
4	chr19:53735800-53756200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr19:53736200-53749000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
6	chr19:53737400-53757600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr19:53738600-53749000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr19:53738800-53756600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
9	chr19:53739400-53743400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
10	chr19:53739400-53755200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr19:53739600-53748600	ZNF genes & repeats	Brain Anterior Caudate	brain
12	chr19:53739600-53748600	ZNF genes & repeats	Brain Germinal Matrix	brain
13	chr19:53739600-53756200	ZNF genes & repeats	Fetal Brain Female	brain
14	chr19:53740000-53747200	ZNF genes & repeats	Brain Substantia Nigra	brain
15	chr19:53740000-53749800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
16	chr19:53740000-53750600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr19:53740000-53756400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr19:53740000-53756600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
19	chr19:53740000-53756800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr19:53740200-53748800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
21	chr19:53740200-53748800	ZNF genes & repeats	Primary B cells from cord blood	blood
22	chr19:53740200-53749000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
23	chr19:53740200-53749000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
24	chr19:53740200-53749000	ZNF genes & repeats	Colon Smooth Muscle	Colon
25	chr19:53740200-53750600	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
26	chr19:53740200-53752600	ZNF genes & repeats	Brain Hippocampus Middle	brain
27	chr19:53740200-53756800	ZNF genes & repeats	Fetal Lung	lung
28	chr19:53740200-53757600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr19:53740400-53743400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
30	chr19:53740400-53743400	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
31	chr19:53740400-53745000	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
32	chr19:53740400-53747400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr19:53740400-53747800	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
34	chr19:53740400-53747800	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
35	chr19:53740400-53748600	ZNF genes & repeats	Stomach Smooth Muscle	stomach
36	chr19:53740400-53748800	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr19:53740400-53749000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
38	chr19:53740400-53749000	ZNF genes & repeats	Primary T cells from cord blood	blood
39	chr19:53740400-53749000	ZNF genes & repeats	Brain Cingulate Gyrus	brain
40	chr19:53740400-53749000	ZNF genes & repeats	Dnd41	blood
41	chr19:53740400-53756800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
42	chr19:53740600-53743400	ZNF genes & repeats	Rectal Smooth Muscle	rectum
43	chr19:53740600-53743400	ZNF genes & repeats	NHDF-Ad	bronchial
44	chr19:53740600-53747600	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
45	chr19:53740600-53747800	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
46	chr19:53740600-53748000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
47	chr19:53740600-53750600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
48	chr19:53740800-53748800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
49	chr19:53741200-53743600	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
50	chr19:53741200-53744600	Weak transcription	Stomach Mucosa	stomach

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