Variant report

Variant	rs34358
Chromosome Location	chr5:74965122-74965123
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	chr5:74952495..74954524-chr5:74962216..74966504,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-POLK-2	chr5:74965019-74965208	NONHSAT102216

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10057967	0.90[MEX][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10075465	0.94[ASW][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs10515214	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs16872768	0.84[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2112347	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs253391	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs253411	0.96[CEU][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs253412	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs253414	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34351	0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34359	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34360	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34361	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3797580	0.90[MEX][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3815895	0.81[AFR][1000 genomes]
rs40060	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs42302	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs42854	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4549504	0.81[GIH][hapmap]
rs4604177	0.81[GIH][hapmap]
rs4704230	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6864091	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6874626	0.84[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6881648	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6893029	0.81[AFR][1000 genomes]
rs888786	0.88[ASW][hapmap];1.00[YRI][hapmap];0.80[AFR][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs34358	DMGDH	cis	parietal	SCAN
rs34358	HMGCR	cis	parietal	SCAN
rs34358	ANKRA2	cis	cerebellum	SCAN
rs34358	HMGCR	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	chr5:74957400-74966000	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr5:74957400-74966000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr5:74959200-74965200	Enhancers	Brain Substantia Nigra	brain
5	chr5:74960200-74968600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr5:74960800-74965400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr5:74961000-74976800	Weak transcription	Colon Smooth Muscle	Colon
8	chr5:74961000-74987800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr5:74961200-74968000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:74962000-74979400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr5:74962200-74965200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:74963000-74966000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr5:74963000-74989800	Weak transcription	Esophagus	oesophagus
14	chr5:74963200-74965400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr5:74963200-74976600	Weak transcription	HMEC	breast
16	chr5:74963400-74968600	Weak transcription	Fetal Lung	lung
17	chr5:74963400-74968600	Weak transcription	Ovary	ovary
18	chr5:74963800-74968200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr5:74964000-74965800	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr5:74964000-74968200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr5:74964200-74965200	Enhancers	Brain Germinal Matrix	brain
22	chr5:74964200-74965200	Enhancers	Fetal Muscle Trunk	muscle
23	chr5:74964200-74965400	Enhancers	Fetal Muscle Leg	muscle
24	chr5:74964200-74965400	Enhancers	Lung	lung
25	chr5:74964200-74965600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr5:74964200-74965600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr5:74964200-74965600	Enhancers	Stomach Mucosa	stomach
28	chr5:74964200-74966000	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr5:74964400-74965200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr5:74964400-74965200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr5:74964400-74965400	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr5:74964400-74965400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr5:74964400-74965400	Flanking Active TSS	HepG2	liver
34	chr5:74964400-74965600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr5:74964400-74965600	Enhancers	Gastric	stomach
36	chr5:74964400-74965600	Enhancers	Spleen	Spleen
37	chr5:74964400-74966000	Flanking Active TSS	GM12878-XiMat	blood
38	chr5:74964400-74967400	Enhancers	Fetal Kidney	kidney
39	chr5:74964600-74965200	Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr5:74964600-74965200	Flanking Active TSS	Duodenum Mucosa	Duodenum
41	chr5:74964600-74965400	Flanking Active TSS	Primary hematopoietic stem cells	blood
42	chr5:74964600-74965400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
43	chr5:74964600-74965400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
44	chr5:74964600-74965400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr5:74964600-74965400	Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr5:74964600-74965600	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr5:74964600-74965600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
48	chr5:74964600-74965600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
49	chr5:74964600-74965600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr5:74964600-74965600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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