Variant report

Variant	rs4859423
Chromosome Location	chr4:77031022-77031023
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10033843	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11097237	1.00[ASN][1000 genomes]
rs1127705	0.91[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12499900	0.85[JPT][hapmap];0.86[YRI][hapmap]
rs12510869	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13130116	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13134121	0.87[YRI][hapmap]
rs13136760	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13141802	0.81[ASN][1000 genomes]
rs17001357	0.92[YRI][hapmap]
rs17001409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17001416	0.89[JPT][hapmap];0.93[YRI][hapmap];0.81[ASN][1000 genomes]
rs34978911	0.81[ASN][1000 genomes]
rs35713908	0.81[ASN][1000 genomes]
rs4077787	0.92[YRI][hapmap]
rs4241584	0.97[GIH][hapmap]
rs4859422	0.84[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4859425	0.85[ASW][hapmap];0.82[JPT][hapmap];0.89[YRI][hapmap];0.80[ASN][1000 genomes]
rs4859426	0.89[JPT][hapmap]
rs4859617	0.80[ASN][1000 genomes]
rs4859618	0.80[ASN][1000 genomes]
rs59050354	0.81[ASN][1000 genomes]
rs7673428	0.82[ASN][1000 genomes]
rs7682766	0.83[ASW][hapmap]
rs7689378	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529613	chr4:76654941-77081576	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1009047	chr4:76989180-77077885	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4859423	MTHFD2L	cis	parietal	SCAN
rs4859423	NUP54	cis	parietal	SCAN
rs4859423	THAP6	cis	cerebellum	SCAN
rs4859423	ANKRD56	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:77017000-77034400	Weak transcription	Right Ventricle	heart
2	chr4:77024000-77032200	Weak transcription	Left Ventricle	heart
3	chr4:77026400-77033400	Weak transcription	HSMMtube	muscle
4	chr4:77026600-77033400	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr4:77027200-77033000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr4:77027200-77033400	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr4:77027200-77034000	Weak transcription	Brain Anterior Caudate	brain
8	chr4:77027200-77034400	Weak transcription	Fetal Muscle Leg	muscle
9	chr4:77027200-77035400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr4:77027600-77033400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr4:77027600-77034200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr4:77027600-77034400	Weak transcription	Brain Hippocampus Middle	brain
13	chr4:77027600-77037400	Weak transcription	Brain Substantia Nigra	brain
14	chr4:77027800-77034200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr4:77027800-77034200	Weak transcription	Fetal Brain Female	brain
16	chr4:77027800-77036400	Weak transcription	Brain Angular Gyrus	brain
17	chr4:77027800-77038400	Weak transcription	Fetal Brain Male	brain
18	chr4:77028000-77033200	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr4:77028000-77034000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:77028000-77037600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr4:77028000-77068600	Weak transcription	Gastric	stomach
22	chr4:77028400-77033200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr4:77028400-77033400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr4:77028400-77034400	Weak transcription	K562	blood
25	chr4:77029200-77033800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr4:77029600-77033400	Weak transcription	HSMM	muscle
27	chr4:77030000-77033400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr4:77030000-77033400	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr4:77030000-77034400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr4:77030000-77037400	Weak transcription	NHDF-Ad	bronchial
31	chr4:77030400-77033400	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr4:77030600-77033400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr4:77030600-77033400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr4:77030600-77034000	Weak transcription	GM12878-XiMat	blood
35	chr4:77030600-77036400	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr4:77030600-77038400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr4:77030800-77033000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr4:77030800-77033400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr4:77030800-77034200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr4:77030800-77034400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr4:77031000-77034200	Weak transcription	HUVEC	blood vessel

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