Variant report

Variant	rs1057603
Chromosome Location	chr7:56108410-56108411
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs13226516	0.82[AMR][1000 genomes]
rs62457265	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62457285	0.85[AMR][1000 genomes]
rs6593296	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829874	chr7:55382925-56369816	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv995105	chr7:55606107-56174888	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	esv12412	chr7:55619800-56385412	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv949574	chr7:55705566-56544711	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	esv3446617	chr7:55745934-56485903	Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
6	nsv529162	chr7:55800753-56174888	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	esv2761334	chr7:55823581-56424739	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
8	nsv1018806	chr7:55844931-56383936	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
9	nsv538860	chr7:55844931-56383936	Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
10	nsv498114	chr7:55872850-56174888	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1057603	LOC146325	trans	lymphoblastoid	RTeQTL
rs1057603	CHCHD2	Cis_1M	lymphoblastoid	RTeQTL
rs1057603	CHCHD2	cis	multi-tissue	Pritchard
rs1057603	CHCHD2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56102200-56108600	Weak transcription	Lung	lung
2	chr7:56102200-56114600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr7:56102200-56117600	Weak transcription	Gastric	stomach
4	chr7:56102200-56117600	Weak transcription	Spleen	Spleen
5	chr7:56102200-56117800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr7:56102200-56118200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr7:56102400-56108600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr7:56102400-56109200	Weak transcription	Fetal Stomach	stomach
9	chr7:56102400-56109400	Weak transcription	Placenta	Placenta
10	chr7:56102400-56109400	Weak transcription	Ovary	ovary
11	chr7:56102400-56110000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr7:56102400-56110000	Weak transcription	Fetal Muscle Leg	muscle
13	chr7:56102400-56110000	Weak transcription	NHEK	skin
14	chr7:56102400-56110200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr7:56102400-56114000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr7:56102400-56114200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr7:56102400-56114200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr7:56102400-56114200	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr7:56102400-56114200	Weak transcription	Colon Smooth Muscle	Colon
20	chr7:56102400-56114200	Weak transcription	Fetal Lung	lung
21	chr7:56102400-56114200	Weak transcription	HUVEC	blood vessel
22	chr7:56102400-56114200	Weak transcription	K562	blood
23	chr7:56102400-56114200	Weak transcription	Osteobl	bone
24	chr7:56102400-56114600	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr7:56102400-56117600	Weak transcription	Brain Anterior Caudate	brain
26	chr7:56102400-56117600	Weak transcription	GM12878-XiMat	blood
27	chr7:56102400-56117800	Weak transcription	Adipose Nuclei	Adipose
28	chr7:56102400-56117800	Weak transcription	Brain Substantia Nigra	brain
29	chr7:56102400-56118000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr7:56102400-56118000	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr7:56102400-56118000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr7:56102400-56118000	Weak transcription	Left Ventricle	heart
33	chr7:56102400-56118000	Weak transcription	HSMMtube	muscle
34	chr7:56102400-56118000	Weak transcription	NHLF	lung
35	chr7:56102400-56118200	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr7:56102600-56108600	Weak transcription	Esophagus	oesophagus
37	chr7:56102600-56109000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr7:56102600-56110000	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr7:56102600-56110000	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr7:56102600-56110000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr7:56102600-56110000	Weak transcription	Primary T cells from cord blood	blood
42	chr7:56102600-56110000	Weak transcription	Primary hematopoietic stem cells	blood
43	chr7:56102600-56110000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr7:56102600-56110000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr7:56102600-56110000	Weak transcription	Liver	Liver
46	chr7:56102600-56110000	Weak transcription	Stomach Smooth Muscle	stomach
47	chr7:56102600-56114200	Weak transcription	HSMM	muscle
48	chr7:56102600-56114600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr7:56102600-56114600	Weak transcription	NH-A	brain
50	chr7:56102600-56114800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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