Variant report

Variant	rs253388
Chromosome Location	chr5:74975912-74975913
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:74969854..74971391-chr5:74974162..74975941,2	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10462356	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10462521	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11746063	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11748378	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs166183	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16872770	0.85[YRI][hapmap]
rs16872776	0.88[YRI][hapmap]
rs17563686	0.86[CEU][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17563863	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17649055	1.00[ASW][hapmap];0.86[CEU][hapmap];0.98[GIH][hapmap];0.91[LWK][hapmap];0.93[MEX][hapmap];0.84[TSI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1817869	0.86[CEU][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs193344	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs194137	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2047059	0.85[EUR][1000 genomes]
rs2307113	1.00[ASW][hapmap];0.86[CEU][hapmap];0.81[GIH][hapmap];0.83[LWK][hapmap];0.93[MEX][hapmap];0.84[TSI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs253387	0.84[ASN][1000 genomes]
rs253389	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs253390	0.86[CEU][hapmap];0.98[GIH][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes]
rs34355	0.91[CHD][hapmap];0.84[ASN][1000 genomes]
rs34356	0.80[JPT][hapmap];0.84[ASN][1000 genomes]
rs34357	0.91[CHD][hapmap]
rs34905687	1.00[ASW][hapmap];0.86[CEU][hapmap];0.81[GIH][hapmap];0.91[LWK][hapmap];0.93[MEX][hapmap];0.84[TSI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs40059	0.83[CHB][hapmap];0.93[JPT][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs41534344	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4703678	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4703679	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4703680	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4704231	1.00[ASW][hapmap];0.86[CEU][hapmap];0.98[GIH][hapmap];0.93[MEX][hapmap];0.93[MKK][hapmap];0.84[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4704234	0.86[CEU][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59778668	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs60134294	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs60423072	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61173369	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs66493518	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67054144	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs67803720	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6868069	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6894099	0.88[YRI][hapmap]
rs72633978	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72633979	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7381033	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs979182	0.84[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv522003	chr5:74947435-74988369	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	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
6	esv1797759	chr5:74973241-74984269	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs253388	HMGCR	cis	cerebellum	SCAN
rs253388	DMGDH	cis	parietal	SCAN
rs253388	TNPO1	cis	cerebellum	SCAN
rs253388	ANKRA2	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74952800-74981400	Weak transcription	Psoas Muscle	Psoas
2	chr5:74961000-74976800	Weak transcription	Colon Smooth Muscle	Colon
3	chr5:74961000-74987800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr5:74962000-74979400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr5:74963000-74989800	Weak transcription	Esophagus	oesophagus
6	chr5:74963200-74976600	Weak transcription	HMEC	breast
7	chr5:74964800-74989400	Weak transcription	HSMMtube	muscle
8	chr5:74965000-74976600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr5:74965000-74977000	Weak transcription	Brain Angular Gyrus	brain
10	chr5:74965000-74978600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr5:74965000-74979800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr5:74965000-74983800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr5:74965000-74991200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr5:74965000-74998000	Weak transcription	Fetal Brain Female	brain
15	chr5:74965200-74977000	Weak transcription	NHLF	lung
16	chr5:74965200-75011800	Weak transcription	Brain Germinal Matrix	brain
17	chr5:74965400-74977000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr5:74965400-74977000	Weak transcription	NH-A	brain
19	chr5:74965400-74978000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr5:74965400-74979400	Weak transcription	Brain Anterior Caudate	brain
21	chr5:74965400-74980600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr5:74965400-74980800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr5:74965400-74981000	Weak transcription	Lung	lung
24	chr5:74965400-74997800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr5:74965400-75012400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr5:74965400-75012400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr5:74965400-75012400	Weak transcription	Right Ventricle	heart
28	chr5:74965600-74978400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr5:74965600-74979400	Weak transcription	Spleen	Spleen
30	chr5:74965600-74979600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr5:74965600-74980800	Weak transcription	Pancreas	Pancrea
32	chr5:74965600-74998200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr5:74965600-74998200	Weak transcription	Fetal Heart	heart
34	chr5:74965600-75010400	Weak transcription	Gastric	stomach
35	chr5:74965600-75011400	Weak transcription	Small Intestine	intestine
36	chr5:74965800-74976600	Weak transcription	Osteobl	bone
37	chr5:74965800-74991800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr5:74966000-74979400	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr5:74966000-74991000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr5:74966000-74998400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr5:74967200-74989600	Weak transcription	Hela-S3	cervix
42	chr5:74967400-74976800	Weak transcription	NHDF-Ad	bronchial
43	chr5:74968800-74983400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr5:74968800-74983800	Weak transcription	Placenta	Placenta
45	chr5:74968800-74998400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr5:74969000-74991600	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr5:74969200-74977800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr5:74969200-74979600	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr5:74969400-74976600	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr5:74969400-74976800	Weak transcription	NHEK	skin

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