Variant report

Variant	rs2047059
Chromosome Location	chr5:75008193-75008194
allele	A/G
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	CEBPB	chr5:75008032-75008197	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:75006833..75009692-chr5:75010741..75014580,11	K562	blood:
2	chr5:75004216..75010579-chr5:75011703..75014378,6	MCF-7	breast:

Variant related genes	Relation type
RNU6-680P	TF binding region
ENSG00000152359	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	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10462521	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11746063	0.81[AMR][1000 genomes]
rs11748378	0.81[AMR][1000 genomes]
rs166183	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17563686	0.91[CEU][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17563863	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17649055	0.91[CEU][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1817869	0.91[CEU][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs193344	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs194137	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2307113	0.91[CEU][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs253388	0.85[EUR][1000 genomes]
rs253389	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs253390	0.94[ASW][hapmap];0.91[CEU][hapmap];0.81[GIH][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];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34905687	0.91[CEU][hapmap];0.81[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs40059	0.85[EUR][1000 genomes]
rs41534344	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4703678	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4703679	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4703680	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4704231	0.91[CEU][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4704234	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]
rs59778668	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60134294	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60423072	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61173369	0.88[EUR][1000 genomes]
rs66493518	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs66787104	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs67054144	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs67803720	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6868069	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72633978	0.85[EUR][1000 genomes]
rs72633979	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7381033	0.89[EUR][1000 genomes]
rs7730516	0.84[JPT][hapmap]

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
rs2047059	ANKRA2	cis	cerebellum	SCAN
rs2047059	DMGDH	cis	parietal	SCAN
rs2047059	HMGCR	cis	cerebellum	SCAN

Chromatin state (count:123 , 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	chr5:74980000-75012200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr5:74984200-75012400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr5:74990000-75012000	Weak transcription	HSMMtube	muscle
12	chr5:74990000-75012400	Weak transcription	Esophagus	oesophagus
13	chr5:74992000-75012400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr5:74992600-75012600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr5:74996800-75012400	Weak transcription	Fetal Brain Male	brain
16	chr5:74997600-75010200	Strong transcription	Dnd41	blood
17	chr5:74997600-75011000	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr5:74998200-75010400	Weak transcription	Lung	lung
19	chr5:74998200-75011600	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr5:74998200-75012400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr5:74998400-75011400	Weak transcription	HepG2	liver
22	chr5:74998600-75010400	Weak transcription	Spleen	Spleen
23	chr5:74998600-75011600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr5:74998600-75011600	Weak transcription	NHLF	lung
25	chr5:74998800-75011400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr5:74998800-75011400	Weak transcription	Fetal Heart	heart
27	chr5:74998800-75011800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr5:74998800-75012000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr5:74998800-75012000	Weak transcription	Brain Anterior Caudate	brain
30	chr5:74998800-75012200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr5:74999000-75011400	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr5:74999000-75011400	Weak transcription	Hela-S3	cervix
33	chr5:74999000-75011600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr5:74999000-75011600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr5:74999000-75011800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr5:74999000-75011800	Weak transcription	Colon Smooth Muscle	Colon
37	chr5:74999000-75011800	Weak transcription	Rectal Smooth Muscle	rectum
38	chr5:74999000-75012000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr5:74999000-75012200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr5:74999000-75012200	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr5:74999000-75012400	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr5:74999000-75012400	Weak transcription	Colonic Mucosa	Colon
43	chr5:74999200-75011400	Weak transcription	Fetal Lung	lung
44	chr5:74999600-75011400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr5:74999800-75011600	Weak transcription	HMEC	breast
46	chr5:74999800-75012400	Weak transcription	Right Atrium	heart
47	chr5:75000000-75009600	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr5:75000400-75011600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr5:75000400-75011800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr5:75000400-75012200	Weak transcription	H1 Cell Line	embryonic stem cell

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