Variant report

Variant	rs34978911
Chromosome Location	chr4:77032284-77032285
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:77031133..77035310-chr4:77057270..77059295,3	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10033843	0.81[ASN][1000 genomes]
rs11097237	0.81[ASN][1000 genomes]
rs1127705	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12499900	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12510869	0.80[ASN][1000 genomes]
rs12641529	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12645639	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12646166	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12648162	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12648709	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13130116	0.81[ASN][1000 genomes]
rs13141802	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17001409	0.80[ASN][1000 genomes]
rs17001416	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2053486	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28590424	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34022163	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs35713908	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36081173	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4859423	0.81[ASN][1000 genomes]
rs4859424	0.82[ASN][1000 genomes]
rs4859425	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859617	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4859618	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59050354	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61153596	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66599877	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6824367	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs72870920	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7673428	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7689378	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs894244	0.87[AMR][1000 genomes];0.94[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs34978911	NUP54	cis	Esophagus Muscularis	GTEx

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:77017000-77034400	Weak transcription	Right Ventricle	heart
2	chr4:77026400-77033400	Weak transcription	HSMMtube	muscle
3	chr4:77026600-77033400	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr4:77027200-77033000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr4:77027200-77033400	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr4:77027200-77034000	Weak transcription	Brain Anterior Caudate	brain
7	chr4:77027200-77034400	Weak transcription	Fetal Muscle Leg	muscle
8	chr4:77027200-77035400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr4:77027600-77033400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr4:77027600-77034200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr4:77027600-77034400	Weak transcription	Brain Hippocampus Middle	brain
12	chr4:77027600-77037400	Weak transcription	Brain Substantia Nigra	brain
13	chr4:77027800-77034200	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr4:77027800-77034200	Weak transcription	Fetal Brain Female	brain
15	chr4:77027800-77036400	Weak transcription	Brain Angular Gyrus	brain
16	chr4:77027800-77038400	Weak transcription	Fetal Brain Male	brain
17	chr4:77028000-77033200	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr4:77028000-77034000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:77028000-77037600	Weak transcription	Brain Cingulate Gyrus	brain
20	chr4:77028000-77068600	Weak transcription	Gastric	stomach
21	chr4:77028400-77033200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr4:77028400-77033400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr4:77028400-77034400	Weak transcription	K562	blood
24	chr4:77029200-77033800	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr4:77029600-77033400	Weak transcription	HSMM	muscle
26	chr4:77030000-77033400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr4:77030000-77033400	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr4:77030000-77034400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr4:77030000-77037400	Weak transcription	NHDF-Ad	bronchial
30	chr4:77030400-77033400	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr4:77030600-77033400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr4:77030600-77033400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr4:77030600-77034000	Weak transcription	GM12878-XiMat	blood
34	chr4:77030600-77036400	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr4:77030600-77038400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr4:77030800-77033000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr4:77030800-77033400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr4:77030800-77034200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr4:77030800-77034400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr4:77031000-77034200	Weak transcription	HUVEC	blood vessel
41	chr4:77031200-77033000	Weak transcription	Primary B cells from peripheral blood	blood
42	chr4:77031200-77033400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr4:77031200-77033400	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr4:77031200-77034000	Weak transcription	NH-A	brain
45	chr4:77031200-77034200	Weak transcription	Osteobl	bone
46	chr4:77031200-77037800	Weak transcription	NHLF	lung
47	chr4:77031400-77033000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr4:77031400-77033200	Weak transcription	Liver	Liver
49	chr4:77031400-77033200	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr4:77031400-77033400	Weak transcription	Primary T helper cells fromperipheralblood	blood

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