Variant report

Variant	rs6892146
Chromosome Location	chr5:74971990-74971991
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:74967624..74970426-chr5:74970966..74973992,3	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10038319	0.89[ASN][1000 genomes]
rs10066858	0.86[CHB][hapmap];0.89[ASN][1000 genomes]
rs10075465	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10515214	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872760	0.87[CHB][hapmap];0.91[CHD][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs16872768	0.83[CHB][hapmap]
rs1862219	0.87[CHB][hapmap];0.91[CHD][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs1862220	0.87[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs2193989	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2193990	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2193991	0.87[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs2216572	0.87[CHB][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs2303647	0.84[CHD][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs253411	0.83[YRI][hapmap]
rs253412	0.92[YRI][hapmap]
rs253414	0.83[ASW][hapmap];0.92[YRI][hapmap]
rs34351	0.88[YRI][hapmap]
rs3815894	0.89[ASN][1000 genomes]
rs3815895	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs42302	1.00[YRI][hapmap]
rs56676015	0.89[ASN][1000 genomes]
rs6893029	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7713211	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs888786	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs888787	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs888897	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6892146	HMGCR	cis	parietal	SCAN
rs6892146	POC5	cis	cerebellum	SCAN
rs6892146	POC5	cis	parietal	SCAN
rs6892146	ZNF366	cis	parietal	SCAN
rs6892146	FLJ35779	cis	multi-tissue	Pritchard

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	chr5:74965600-74973000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr5:74965600-74978400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr5:74965600-74979400	Weak transcription	Spleen	Spleen
31	chr5:74965600-74979600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr5:74965600-74980800	Weak transcription	Pancreas	Pancrea
33	chr5:74965600-74998200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr5:74965600-74998200	Weak transcription	Fetal Heart	heart
35	chr5:74965600-75010400	Weak transcription	Gastric	stomach
36	chr5:74965600-75011400	Weak transcription	Small Intestine	intestine
37	chr5:74965800-74973600	Weak transcription	HepG2	liver
38	chr5:74965800-74976600	Weak transcription	Osteobl	bone
39	chr5:74965800-74991800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr5:74966000-74973600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr5:74966000-74979400	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr5:74966000-74991000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr5:74966000-74998400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr5:74967200-74989600	Weak transcription	Hela-S3	cervix
45	chr5:74967400-74976800	Weak transcription	NHDF-Ad	bronchial
46	chr5:74967600-74972400	Strong transcription	GM12878-XiMat	blood
47	chr5:74967800-74975200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr5:74968000-74972600	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr5:74968000-74974000	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr5:74968200-74972000	Strong transcription	Duodenum Mucosa	Duodenum

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