Variant report

Variant	rs13116789
Chromosome Location	chr4:120415212-120415213
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:120408558-120415708	IMR90	lung:	n/a	n/a

Variant related genes	Relation type
ENSG00000245958	TF binding region

Extended variants
information (count: 64 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10025536	0.85[EUR][1000 genomes]
rs11724055	1.00[CHB][hapmap]
rs11730798	0.85[EUR][1000 genomes]
rs11731568	0.85[EUR][1000 genomes]
rs11734808	0.93[CEU][hapmap];1.00[CHB][hapmap]
rs13103510	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs13103899	1.00[CHB][hapmap]
rs13106925	0.85[JPT][hapmap];0.85[EUR][1000 genomes]
rs13107334	0.81[EUR][1000 genomes]
rs13118388	0.85[EUR][1000 genomes]
rs13120581	0.85[JPT][hapmap];0.85[EUR][1000 genomes]
rs13121569	1.00[CHB][hapmap]
rs13124532	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13127517	0.93[CEU][hapmap];1.00[CHB][hapmap]
rs13136296	0.85[EUR][1000 genomes]
rs13137511	0.85[EUR][1000 genomes]
rs1397611	0.93[CEU][hapmap];1.00[CHB][hapmap]
rs17050312	0.93[CEU][hapmap];1.00[CHB][hapmap]
rs17292047	1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes]
rs17358524	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs17358860	1.00[CHB][hapmap]
rs2389868	0.85[EUR][1000 genomes]
rs2389870	1.00[CHB][hapmap]
rs2953295	0.83[EUR][1000 genomes]
rs34601943	0.85[EUR][1000 genomes]
rs34676199	0.85[EUR][1000 genomes]
rs35264119	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35708340	0.80[AMR][1000 genomes]
rs35850447	0.85[EUR][1000 genomes]
rs35967840	0.85[EUR][1000 genomes]
rs35999787	0.85[EUR][1000 genomes]
rs3756155	0.81[CEU][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes]
rs3775846	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3775850	1.00[CHB][hapmap]
rs3775856	1.00[CHB][hapmap]
rs4833620	0.85[EUR][1000 genomes]
rs4834782	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4834788	0.85[EUR][1000 genomes]
rs4834789	0.85[EUR][1000 genomes]
rs4834790	0.88[JPT][hapmap];0.84[EUR][1000 genomes]
rs62319568	0.80[AMR][1000 genomes]
rs62319574	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62319578	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62319606	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs62319612	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs62319647	0.85[EUR][1000 genomes]
rs62319657	0.85[EUR][1000 genomes]
rs62319658	0.85[EUR][1000 genomes]
rs6817975	0.84[JPT][hapmap];0.85[EUR][1000 genomes]
rs71614451	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs988146	0.87[EUR][1000 genomes];0.91[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	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012868	chr4:120014630-120464880	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv537232	chr4:120014630-120464880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv879842	chr4:120244085-120424087	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv427694	chr4:120250511-120501728	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv879843	chr4:120326323-120502461	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv879844	chr4:120341296-120449810	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv879846	chr4:120341296-120491714	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv879845	chr4:120341296-120502461	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv879847	chr4:120371729-120450159	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv532739	chr4:120392824-121098103	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
12	esv1802153	chr4:120397829-120457682	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv879848	chr4:120408931-120433807	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13116789	RP11-33B1.1	cis	Thyroid	GTEx
rs13116789	USP53	cis	Whole Blood	GTEx
rs13116789	LOC645513	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120376400-120471600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:120376600-120419200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr4:120377000-120416000	Weak transcription	Colon Smooth Muscle	Colon
4	chr4:120377200-120415600	Weak transcription	Brain Substantia Nigra	brain
5	chr4:120377200-120416200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr4:120377200-120419600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr4:120377200-120433800	Weak transcription	Gastric	stomach
8	chr4:120377400-120416200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr4:120377400-120439000	Weak transcription	Small Intestine	intestine
10	chr4:120377400-120439000	Weak transcription	Spleen	Spleen
11	chr4:120377600-120441000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr4:120377600-120501200	Weak transcription	Pancreas	Pancrea
13	chr4:120384400-120439200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr4:120384600-120416200	Weak transcription	Fetal Brain Male	brain
15	chr4:120390800-120419800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr4:120391600-120415600	Weak transcription	HUVEC	blood vessel
17	chr4:120393200-120419800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr4:120397800-120416400	Weak transcription	HSMMtube	muscle
19	chr4:120397800-120442600	Weak transcription	Hela-S3	cervix
20	chr4:120398200-120419600	Weak transcription	Fetal Stomach	stomach
21	chr4:120398800-120420000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:120399200-120431200	Weak transcription	Fetal Heart	heart
23	chr4:120401200-120416200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr4:120401400-120419600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr4:120401400-120419800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr4:120401600-120416000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr4:120401600-120416000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr4:120401600-120419400	Weak transcription	Brain Angular Gyrus	brain
29	chr4:120401600-120433800	Weak transcription	Right Ventricle	heart
30	chr4:120401800-120416200	Weak transcription	Aorta	Aorta
31	chr4:120401800-120416200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr4:120401800-120419000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr4:120401800-120419600	Weak transcription	Lung	lung
34	chr4:120401800-120433400	Weak transcription	Psoas Muscle	Psoas
35	chr4:120402400-120416200	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr4:120402400-120430400	Weak transcription	Ovary	ovary
37	chr4:120403400-120445800	Weak transcription	A549	lung
38	chr4:120403800-120415400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr4:120403800-120415400	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr4:120404000-120419400	Weak transcription	Fetal Kidney	kidney
41	chr4:120404000-120419800	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr4:120404200-120415400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr4:120404400-120416400	Weak transcription	K562	blood
44	chr4:120404400-120419600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr4:120404600-120419000	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr4:120404800-120415400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr4:120404800-120415600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr4:120404800-120415600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr4:120404800-120416200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr4:120406400-120416200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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