Variant report

Variant	rs58571234
Chromosome Location	chr7:56145592-56145593
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs17172508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2192262	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3966180	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4443615	0.83[EUR][1000 genomes]
rs4495378	0.83[EUR][1000 genomes]
rs4948095	0.83[EUR][1000 genomes]
rs4948098	1.00[ASN][1000 genomes]
rs4948103	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4948107	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4948108	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59193297	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59852874	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6593298	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66485869	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66741911	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67818657	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6947109	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6954669	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6955615	0.86[AMR][1000 genomes]
rs73132395	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73132398	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73134793	0.83[EUR][1000 genomes]
rs73134796	0.83[EUR][1000 genomes]
rs73135709	0.84[EUR][1000 genomes]
rs73138732	1.00[ASN][1000 genomes]
rs73138736	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138750	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73140745	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73140778	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7779821	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784730	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7791221	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7806994	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7808487	0.80[EUR][1000 genomes];1.00[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs58571234	CHCHD2	cis	Esophagus Mucosa	GTEx
rs58571234	CHCHD2	cis	Whole Blood	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56131800-56146800	Weak transcription	Fetal Heart	heart
2	chr7:56133200-56145600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:56133200-56146400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr7:56133200-56147000	Weak transcription	Fetal Brain Male	brain
5	chr7:56133200-56147000	Weak transcription	Psoas Muscle	Psoas
6	chr7:56133400-56145800	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr7:56134000-56152000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr7:56134000-56167800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr7:56134200-56167600	Weak transcription	Small Intestine	intestine
10	chr7:56137200-56146000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr7:56138800-56146800	Weak transcription	Aorta	Aorta
12	chr7:56138800-56146800	Weak transcription	HSMMtube	muscle
13	chr7:56138800-56156200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr7:56138800-56167600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr7:56139000-56145600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr7:56139000-56145600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr7:56139000-56146800	Weak transcription	HSMM	muscle
18	chr7:56139000-56147000	Weak transcription	NH-A	brain
19	chr7:56139200-56146400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr7:56139400-56146000	Weak transcription	Primary B cells from cord blood	blood
21	chr7:56139400-56146000	Weak transcription	Brain Angular Gyrus	brain
22	chr7:56140400-56152000	Strong transcription	Dnd41	blood
23	chr7:56140800-56153000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr7:56141000-56145600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr7:56141000-56145800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr7:56141000-56145800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr7:56142000-56145600	Weak transcription	K562	blood
28	chr7:56142000-56151600	Strong transcription	Thymus	Thymus
29	chr7:56142000-56168000	Weak transcription	GM12878-XiMat	blood
30	chr7:56142200-56145600	Weak transcription	Brain Germinal Matrix	brain
31	chr7:56142200-56149600	Weak transcription	Fetal Kidney	kidney
32	chr7:56142200-56167800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr7:56142400-56145600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr7:56142400-56145800	Weak transcription	Gastric	stomach
35	chr7:56142400-56146200	Weak transcription	Rectal Smooth Muscle	rectum
36	chr7:56142400-56146200	Weak transcription	HepG2	liver
37	chr7:56142400-56146600	Weak transcription	Brain Cingulate Gyrus	brain
38	chr7:56142400-56156400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr7:56142600-56145600	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr7:56142600-56145800	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr7:56142600-56145800	Weak transcription	Adipose Nuclei	Adipose
42	chr7:56142600-56145800	Weak transcription	Brain Anterior Caudate	brain
43	chr7:56142600-56145800	Weak transcription	Colonic Mucosa	Colon
44	chr7:56142600-56145800	Weak transcription	Esophagus	oesophagus
45	chr7:56142600-56146200	Weak transcription	Right Atrium	heart
46	chr7:56142600-56146800	Weak transcription	Left Ventricle	heart
47	chr7:56142600-56146800	Weak transcription	Stomach Mucosa	stomach
48	chr7:56142600-56159800	Strong transcription	Fetal Intestine Small	intestine
49	chr7:56142800-56146000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr7:56142800-56146600	Weak transcription	Colon Smooth Muscle	Colon

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