Variant report

Variant	rs4704234
Chromosome Location	chr5:75001432-75001433
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:75001250..75005615-chr5:75010572..75014500,9	K562	blood:
2	chr5:75001323..75004306-chr5:75007634..75010552,4	K562	blood:
3	chr5:74997231..74999217-chr5:75000460..75002166,2	K562	blood:
4	chr5:74999928..75003890-chr5:75004473..75007549,3	K562	blood:

Variant related genes	Relation type
ENSG00000152359	Chromatin interaction
ENSG00000207333	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10462356	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10462521	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11746063	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11748378	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs166183	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17563686	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17563863	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17649055	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17649332	0.89[CHD][hapmap]
rs1817869	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs193344	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs194137	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2047059	0.94[ASW][hapmap];0.91[CEU][hapmap];0.81[JPT][hapmap];0.95[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2307113	1.00[CEU][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs253388	0.86[CEU][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs253389	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs253390	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34905687	1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3797580	0.83[CEU][hapmap]
rs40059	0.84[EUR][1000 genomes]
rs41534344	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4703678	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4703679	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4703680	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4704231	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs59778668	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60134294	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60423072	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61173369	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs66493518	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs67054144	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs67803720	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6868069	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72633978	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72633979	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7381033	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027368	chr5:74759999-75663712	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv518475	chr5:74863041-75411804	Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	esv1850196	chr5:74890618-75138443	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv830353	chr5:74961520-75152609	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4704234	DMGDH	cis	parietal	SCAN
rs4704234	HMGCR	cis	cerebellum	SCAN
rs4704234	TNPO1	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74965200-75011800	Weak transcription	Brain Germinal Matrix	brain
2	chr5:74965400-75012400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:74965400-75012400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr5:74965400-75012400	Weak transcription	Right Ventricle	heart
5	chr5:74965600-75010400	Weak transcription	Gastric	stomach
6	chr5:74965600-75011400	Weak transcription	Small Intestine	intestine
7	chr5:74971200-75012400	Weak transcription	Aorta	Aorta
8	chr5:74971200-75012400	Weak transcription	Brain Substantia Nigra	brain
9	chr5:74979000-75003800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr5:74980000-75012200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr5:74981400-75002600	Weak transcription	Pancreas	Pancrea
12	chr5:74984200-75012400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr5:74986800-75005800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr5:74987800-75002600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr5:74990000-75012000	Weak transcription	HSMMtube	muscle
16	chr5:74990000-75012400	Weak transcription	Esophagus	oesophagus
17	chr5:74992000-75012400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr5:74992400-75005800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr5:74992600-75012600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr5:74996400-75006400	Weak transcription	Stomach Mucosa	stomach
21	chr5:74996800-75012400	Weak transcription	Fetal Brain Male	brain
22	chr5:74997600-75001600	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr5:74997600-75001600	Strong transcription	Liver	Liver
24	chr5:74997600-75001800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr5:74997600-75003200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr5:74997600-75004200	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr5:74997600-75004200	Strong transcription	Primary B cells from peripheral blood	blood
28	chr5:74997600-75004200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr5:74997600-75004400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr5:74997600-75004600	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr5:74997600-75010200	Strong transcription	Dnd41	blood
32	chr5:74997600-75011000	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr5:74998200-75010400	Weak transcription	Lung	lung
34	chr5:74998200-75011600	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr5:74998200-75012400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr5:74998400-75011400	Weak transcription	HepG2	liver
37	chr5:74998600-75001800	Weak transcription	GM12878-XiMat	blood
38	chr5:74998600-75005800	Weak transcription	Brain Hippocampus Middle	brain
39	chr5:74998600-75010400	Weak transcription	Spleen	Spleen
40	chr5:74998600-75011600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr5:74998600-75011600	Weak transcription	NHLF	lung
42	chr5:74998800-75002400	Weak transcription	Fetal Intestine Large	intestine
43	chr5:74998800-75005600	Weak transcription	NH-A	brain
44	chr5:74998800-75005800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr5:74998800-75005800	Weak transcription	Fetal Kidney	kidney
46	chr5:74998800-75005800	Weak transcription	Ovary	ovary
47	chr5:74998800-75006200	Weak transcription	Left Ventricle	heart
48	chr5:74998800-75007600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr5:74998800-75011400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr5:74998800-75011400	Weak transcription	Fetal Heart	heart

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