Variant report

Variant	rs2013979
Chromosome Location	chr5:58612733-58612734
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	chr5:58605150..58607520-chr5:58610737..58612919,2	K562	blood:

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10940644	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs11744761	0.81[ASN][1000 genomes]
rs11959132	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs12189022	0.83[ASN][1000 genomes]
rs1445954	0.81[CHD][hapmap]
rs1840846	0.83[ASN][1000 genomes]
rs2014012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4700328	0.81[CHD][hapmap]
rs6877508	0.81[CHD][hapmap]
rs7703022	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs889231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv598252	chr5:58487764-58618889	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1023628	chr5:58557950-58757438	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv917274	chr5:58565291-58814374	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1030117	chr5:58587672-58637179	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
5	esv2760953	chr5:58609468-58620440	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2013979	NDUFAF2	cis	cerebellum	SCAN
rs2013979	Contig15261_RC	cis	multi-tissue	Pritchard
rs2013979	PDE4D	cis	Liver	GTEx

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58593200-58613400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr5:58594000-58612800	Weak transcription	Stomach Mucosa	stomach
3	chr5:58598000-58612800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:58598000-58612800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr5:58605000-58612800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:58605200-58612800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr5:58605200-58613000	Weak transcription	Fetal Brain Female	brain
8	chr5:58606800-58612800	Enhancers	Colon Smooth Muscle	Colon
9	chr5:58607800-58616400	Enhancers	Fetal Heart	heart
10	chr5:58610000-58613800	Enhancers	Fetal Muscle Leg	muscle
11	chr5:58610200-58612800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr5:58610600-58613000	Enhancers	Hela-S3	cervix
13	chr5:58611200-58613800	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr5:58611400-58613000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr5:58611400-58613000	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr5:58611600-58612800	Weak transcription	Gastric	stomach
17	chr5:58611600-58612800	Weak transcription	A549	lung
18	chr5:58611800-58612800	Weak transcription	Spleen	Spleen
19	chr5:58611800-58613600	Enhancers	HSMMtube	muscle
20	chr5:58612200-58612800	Enhancers	Rectal Smooth Muscle	rectum
21	chr5:58612400-58613000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr5:58612400-58613400	Enhancers	Right Atrium	heart
23	chr5:58612400-58613600	Enhancers	Left Ventricle	heart
24	chr5:58612400-58613600	Enhancers	Right Ventricle	heart
25	chr5:58612400-58613800	Enhancers	Psoas Muscle	Psoas
26	chr5:58612400-58614200	Enhancers	Fetal Kidney	kidney
27	chr5:58612400-58616200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr5:58612600-58612800	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr5:58612600-58612800	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr5:58612600-58612800	Enhancers	Aorta	Aorta
31	chr5:58612600-58612800	Enhancers	Stomach Smooth Muscle	stomach
32	chr5:58612600-58613000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr5:58612600-58613000	Enhancers	Colonic Mucosa	Colon
34	chr5:58612600-58613200	Enhancers	Pancreatic Islets	Pancreatic Islet
35	chr5:58612600-58613200	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr5:58612600-58613400	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr5:58612600-58613400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr5:58612600-58613400	Enhancers	Placenta	Placenta
39	chr5:58612600-58613600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr5:58612600-58613600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr5:58612600-58613600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
42	chr5:58612600-58613600	Enhancers	Small Intestine	intestine
43	chr5:58612600-58613600	Enhancers	HSMM	muscle
44	chr5:58612600-58613800	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr5:58612600-58613800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr5:58612600-58613800	Enhancers	Fetal Intestine Large	intestine
47	chr5:58612600-58613800	Enhancers	Ovary	ovary
48	chr5:58612600-58614000	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr5:58612600-58614000	Enhancers	Brain Anterior Caudate	brain
50	chr5:58612600-58614000	Enhancers	Brain Hippocampus Middle	brain

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