Variant report

Variant	rs34357
Chromosome Location	chr5:74964128-74964129
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10515213	0.83[CEU][hapmap];0.94[GIH][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs168807	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs17563589	0.87[EUR][1000 genomes]
rs17563610	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs17563700	0.85[EUR][1000 genomes]
rs17563877	0.83[CEU][hapmap];0.94[GIH][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs17563974	0.84[EUR][1000 genomes]
rs17563995	0.87[EUR][1000 genomes]
rs17649248	0.83[CEU][hapmap];0.94[GIH][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs17649266	0.83[CEU][hapmap];0.94[GIH][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs17649332	0.83[CEU][hapmap];0.91[GIH][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs17649350	0.83[CEU][hapmap];0.94[GIH][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs17649362	0.87[EUR][1000 genomes]
rs2291630	0.83[CEU][hapmap];0.94[GIH][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs2307112	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs2307115	0.85[EUR][1000 genomes]
rs253387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs253388	0.91[CHD][hapmap];0.84[ASN][1000 genomes]
rs253410	0.94[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34339	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34342	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34343	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34349	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34355	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797581	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs4703676	0.87[EUR][1000 genomes]
rs4704229	0.81[CHD][hapmap]
rs4704233	0.83[EUR][1000 genomes]
rs5744544	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs5744545	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs5744712	0.84[CHD][hapmap];0.82[MEX][hapmap]
rs58255973	0.86[EUR][1000 genomes]
rs58968428	0.84[EUR][1000 genomes]
rs6891560	0.81[CHD][hapmap]
rs72633977	0.80[ASN][1000 genomes]
rs72633981	0.84[EUR][1000 genomes]
rs72633982	0.84[EUR][1000 genomes]
rs72633983	0.84[EUR][1000 genomes]
rs72633984	0.82[EUR][1000 genomes]
rs72633985	0.84[EUR][1000 genomes]
rs72633986	0.84[EUR][1000 genomes]
rs72633987	0.87[EUR][1000 genomes]
rs72633988	0.87[EUR][1000 genomes]
rs72633989	0.86[EUR][1000 genomes]
rs72633990	0.86[EUR][1000 genomes]
rs7380748	0.81[EUR][1000 genomes]
rs888788	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs9293655	0.81[CHD][hapmap]
rs979182	0.93[CHD][hapmap];1.00[JPT][hapmap]

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
rs34357	FLJ35779	cis	multi-tissue	Pritchard
rs34357	TNPO1	cis	cerebellum	SCAN
rs34357	POC5	cis	Thyroid	GTEx
rs34357	POC5	cis	cerebellum	SCAN
rs34357	HMGCR	cis	cerebellum	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74921800-74964400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:74952600-74964200	Weak transcription	Stomach Mucosa	stomach
3	chr5:74952800-74964200	Weak transcription	Right Ventricle	heart
4	chr5:74952800-74964400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr5:74952800-74981400	Weak transcription	Psoas Muscle	Psoas
6	chr5:74953000-74964200	Weak transcription	Fetal Muscle Leg	muscle
7	chr5:74953000-74964400	Weak transcription	Adipose Nuclei	Adipose
8	chr5:74953000-74964400	Weak transcription	Fetal Kidney	kidney
9	chr5:74953000-74964400	Weak transcription	Fetal Stomach	stomach
10	chr5:74953000-74964600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr5:74956000-74965000	Weak transcription	NHEK	skin
12	chr5:74956600-74964400	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr5:74956800-74964600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr5:74957400-74966000	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr5:74957400-74966000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr5:74958000-74964600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr5:74958400-74964400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr5:74959200-74965200	Enhancers	Brain Substantia Nigra	brain
19	chr5:74960200-74968600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr5:74960800-74965400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr5:74961000-74964200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr5:74961000-74976800	Weak transcription	Colon Smooth Muscle	Colon
23	chr5:74961000-74987800	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr5:74961200-74964600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr5:74961200-74965000	Enhancers	Brain Hippocampus Middle	brain
26	chr5:74961200-74968000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr5:74962000-74964200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr5:74962000-74964400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr5:74962000-74979400	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr5:74962200-74965200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr5:74962400-74964200	Weak transcription	Brain Germinal Matrix	brain
32	chr5:74962800-74964600	Strong transcription	Fetal Intestine Large	intestine
33	chr5:74962800-74964800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr5:74962800-74964800	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr5:74963000-74964600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr5:74963000-74964800	Enhancers	Brain Anterior Caudate	brain
37	chr5:74963000-74966000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr5:74963000-74989800	Weak transcription	Esophagus	oesophagus
39	chr5:74963200-74964200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr5:74963200-74964200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr5:74963200-74964600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr5:74963200-74965000	Enhancers	Brain Angular Gyrus	brain
43	chr5:74963200-74965000	Enhancers	Brain Cingulate Gyrus	brain
44	chr5:74963200-74965400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr5:74963200-74976600	Weak transcription	HMEC	breast
46	chr5:74963400-74964200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr5:74963400-74964400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr5:74963400-74964400	Weak transcription	Left Ventricle	heart
49	chr5:74963400-74968600	Weak transcription	Fetal Lung	lung
50	chr5:74963400-74968600	Weak transcription	Ovary	ovary

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