Variant report

Variant	rs378074
Chromosome Location	chr5:178682067-178682068
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11249618	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11741111	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11743204	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12153128	0.82[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs13155737	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13169156	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs13169291	0.82[ASN][1000 genomes]
rs13178420	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs13179057	0.82[ASN][1000 genomes]
rs13182310	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs173104	0.92[CEU][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17607156	0.93[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2054782	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs338874	0.85[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs338875	0.85[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs338876	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs340120	0.80[ASN][1000 genomes]
rs340124	1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs34756026	0.84[ASN][1000 genomes]
rs35870414	0.84[ASN][1000 genomes]
rs35996372	0.84[ASN][1000 genomes]
rs467017	0.83[CEU][hapmap];0.91[EUR][1000 genomes]
rs467604	0.96[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs468723	0.85[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs469262	0.84[CEU][hapmap];0.92[EUR][1000 genomes]
rs469290	0.92[EUR][1000 genomes]
rs469396	0.82[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4700789	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4700790	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs4701085	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs62394987	0.86[ASN][1000 genomes]
rs6601023	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6601024	0.82[ASN][1000 genomes]
rs6868427	0.82[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024560	chr5:178415364-178917595	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv537975	chr5:178415364-178917595	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv817413	chr5:178415365-179020558	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	nsv1033597	chr5:178423101-178752095	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1026790	chr5:178511268-178687428	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv482352	chr5:178525060-178697496	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1016097	chr5:178544084-178866001	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1026968	chr5:178545479-178865895	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv537976	chr5:178545479-178865895	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv600496	chr5:178552518-178752351	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv883228	chr5:178604465-178796142	Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
12	nsv883231	chr5:178614867-178813207	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv830558	chr5:178624391-178805604	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv883232	chr5:178626437-178805612	Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv1018641	chr5:178627012-178911254	ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
16	nsv537978	chr5:178627012-178911254	Flanking Bivalent TSS/Enh Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
17	nsv462575	chr5:178639040-178686438	ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
18	nsv600497	chr5:178639040-178686438	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
19	nsv462576	chr5:178645310-178698709	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
20	nsv600498	chr5:178645310-178698709	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
21	nsv462577	chr5:178645310-178706162	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
22	nsv600499	chr5:178645310-178706162	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
23	nsv462578	chr5:178659691-178713712	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
24	nsv600500	chr5:178659691-178713712	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
25	esv2758031	chr5:178661266-179037529	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
26	esv2759397	chr5:178661266-179037529	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
27	nsv531996	chr5:178669297-178989687	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
28	nsv883233	chr5:178675065-178746447	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs378074	ZNF346	cis	parietal	SCAN
rs378074	RMND5B	cis	cerebellum	SCAN
rs378074	PROP1	cis	cerebellum	SCAN
rs378074	CLTB	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178670000-178691800	Weak transcription	Right Atrium	heart
2	chr5:178670600-178682800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:178671200-178682600	Weak transcription	Fetal Stomach	stomach
4	chr5:178671200-178686400	Weak transcription	Fetal Lung	lung
5	chr5:178671400-178685200	Weak transcription	HSMMtube	muscle
6	chr5:178672200-178682600	Weak transcription	NHLF	lung
7	chr5:178673800-178684200	Weak transcription	Adipose Nuclei	Adipose
8	chr5:178675400-178682200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr5:178675600-178682400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr5:178677600-178685400	Weak transcription	HSMM	muscle
11	chr5:178678000-178682400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr5:178681000-178682200	Weak transcription	Spleen	Spleen
13	chr5:178681400-178682600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr5:178681600-178682200	Enhancers	Brain Angular Gyrus	brain
15	chr5:178681600-178682200	Enhancers	Brain Hippocampus Middle	brain
16	chr5:178681600-178682600	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr5:178681600-178682600	Enhancers	Brain Substantia Nigra	brain
18	chr5:178681600-178685000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr5:178681800-178682200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr5:178681800-178682200	Enhancers	Brain Anterior Caudate	brain
21	chr5:178681800-178683600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr5:178681800-178684000	Enhancers	Fetal Muscle Trunk	muscle
23	chr5:178681800-178686400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr5:178682000-178682200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr5:178682000-178682200	Weak transcription	Osteobl	bone
26	chr5:178682000-178682400	Weak transcription	Fetal Muscle Leg	muscle
27	chr5:178682000-178683400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr5:178682000-178683800	Strong transcription	Muscle Satellite Cultured Cells	--
29	chr5:178682000-178684000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr5:178682000-178684000	Weak transcription	NHDF-Ad	bronchial

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