Variant report

Variant	rs230819
Chromosome Location	chr5:42805965-42805966
allele	A/C
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	chr5:42805758-42812555	HepG2	liver:	n/a	n/a
2	MBD4	chr5:42804512-42808794	HepG2	liver:	n/a	n/a
3	POLR2A	chr5:42797012-42808716	HepG2	liver:	n/a	n/a
4	POLR2A	chr5:42798272-42812268	HepG2	liver:	n/a	n/a
5	MYBL2	chr5:42805714-42807317	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:42804005..42807710-chr5:42809581..42813463,4	K562	blood:
2	chr5:42804005..42807994-chr5:42809581..42813463,4	K562	blood:

Variant related genes	Relation type
ENSG00000272234	TF binding region
ENSG00000250722	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1074263	0.93[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10941591	0.87[ASN][1000 genomes]
rs10941592	0.82[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs10941593	0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs12517008	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12519532	0.82[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs12521615	0.82[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs13167366	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1345824	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs1345825	0.95[ASN][1000 genomes]
rs1423653	0.93[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1423656	0.89[ASN][1000 genomes]
rs1593071	0.95[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1862628	0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs1862629	0.85[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1862630	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs1895457	0.96[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2014958	0.95[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2113088	0.96[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs230807	0.95[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs230812	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs230813	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs230814	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs230816	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs230820	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2459629	0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2910851	0.95[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2910855	0.95[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2910856	0.95[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2910862	0.95[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2910864	0.95[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2910871	0.95[ASN][1000 genomes]
rs2910875	0.95[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap]
rs2910880	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2910881	0.86[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2972756	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2972757	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2972758	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2972759	0.97[ASN][1000 genomes]
rs2972761	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2972763	0.85[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2972767	0.93[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2972783	0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2972992	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs2972994	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2972998	0.95[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2972999	0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2973000	0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2973001	0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2973006	0.96[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2973011	0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2973015	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2973018	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs2973023	0.95[ASN][1000 genomes]
rs2973028	0.97[ASN][1000 genomes]
rs2973029	0.80[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2973031	0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs34443829	0.88[ASN][1000 genomes]
rs34926728	0.87[ASN][1000 genomes]
rs35293842	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4866800	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs4866801	0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4866802	0.88[ASN][1000 genomes]
rs6179	0.84[LWK][hapmap]
rs6180	0.95[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.88[MEX][hapmap];0.92[ASN][1000 genomes]
rs62370950	0.88[ASN][1000 genomes]
rs62370952	0.88[ASN][1000 genomes]
rs62370955	0.87[ASN][1000 genomes]
rs6882333	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs719756	0.95[ASN][1000 genomes]
rs9637794	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
2	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases
3	nsv1031160	chr5:42610090-42843255	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1019696	chr5:42610090-42844191	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv597886	chr5:42610409-42854408	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1029933	chr5:42611976-42833385	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv537735	chr5:42611976-42833385	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS 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	8 gene(s)	inside rSNPs	diseases
8	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
9	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
10	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
11	nsv523033	chr5:42752037-42919685	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	nsv965602	chr5:42767568-42889585	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
14	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
15	nsv534185	chr5:42804840-43067088	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	165 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs230819	GHR	cis	brain	BrainEAC
rs230819	OXCT1	cis	parietal	SCAN
rs230819	STAG1	trans	parietal	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42788600-42807600	Weak transcription	Primary T cells from cord blood	blood
2	chr5:42789600-42813400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:42791400-42811200	Weak transcription	Fetal Thymus	thymus
4	chr5:42792000-42807600	Weak transcription	NHDF-Ad	bronchial
5	chr5:42795600-42810200	Weak transcription	Thymus	Thymus
6	chr5:42797000-42810600	Weak transcription	Esophagus	oesophagus
7	chr5:42797400-42810800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr5:42797600-42808200	Weak transcription	HSMM	muscle
9	chr5:42797800-42809200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr5:42798200-42808400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr5:42798200-42811200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr5:42798600-42806200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr5:42798600-42808200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr5:42798800-42806200	Weak transcription	Brain Angular Gyrus	brain
15	chr5:42798800-42806400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr5:42799000-42811600	Weak transcription	HSMMtube	muscle
17	chr5:42799400-42807000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr5:42799400-42807400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr5:42799400-42808200	Weak transcription	Colonic Mucosa	Colon
20	chr5:42799600-42807600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr5:42799600-42811400	Weak transcription	Fetal Brain Female	brain
22	chr5:42799600-42812000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:42799800-42806000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr5:42799800-42806200	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr5:42799800-42807400	Strong transcription	Adipose Nuclei	Adipose
26	chr5:42799800-42808200	Strong transcription	Placenta	Placenta
27	chr5:42799800-42808400	Weak transcription	Colon Smooth Muscle	Colon
28	chr5:42800000-42806200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr5:42800000-42808200	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr5:42800000-42809400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr5:42800400-42806600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr5:42800600-42806200	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr5:42800600-42807200	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr5:42800600-42808000	Strong transcription	Skeletal Muscle Male	skeletal muscle
35	chr5:42800600-42811200	Weak transcription	Small Intestine	intestine
36	chr5:42800800-42806800	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr5:42800800-42808200	Weak transcription	Stomach Mucosa	stomach
38	chr5:42801400-42806400	Weak transcription	Rectal Smooth Muscle	rectum
39	chr5:42802000-42809000	Weak transcription	Right Ventricle	heart
40	chr5:42802000-42809600	Weak transcription	Fetal Muscle Leg	muscle
41	chr5:42802000-42810200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr5:42802000-42810200	Weak transcription	Brain Germinal Matrix	brain
43	chr5:42802000-42810600	Weak transcription	Aorta	Aorta
44	chr5:42802000-42810600	Weak transcription	Fetal Muscle Trunk	muscle
45	chr5:42802000-42810600	Weak transcription	Gastric	stomach
46	chr5:42802000-42810600	Weak transcription	Lung	lung
47	chr5:42802000-42811000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr5:42802000-42811200	Weak transcription	Spleen	Spleen
49	chr5:42802200-42810200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr5:42802400-42808200	Weak transcription	Psoas Muscle	Psoas

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