Variant report

Variant	rs6593294
Chromosome Location	chr7:56063201-56063202
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:56032346..56034180-chr7:56063037..56065677,2	K562	blood:
2	chr7:56032680..56034503-chr7:56061910..56064537,2	K562	blood:

Variant related genes	Relation type
ENSG00000146729	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10229446	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10245725	0.87[ASN][1000 genomes]
rs10250964	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10252442	0.87[ASN][1000 genomes]
rs10266902	0.86[ASN][1000 genomes]
rs10271662	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs10272406	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs10435504	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11238389	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11765531	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs11765577	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs13240915	0.89[EUR][1000 genomes]
rs13241866	0.90[EUR][1000 genomes]
rs2135116	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs28636652	0.87[ASN][1000 genomes]
rs28678267	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs28828764	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs34016595	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs35844144	0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4470984	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4535700	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4543497	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4689	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4947533	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4947534	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4948096	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4948097	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4948099	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4948102	0.90[EUR][1000 genomes]
rs57153841	0.87[ASN][1000 genomes]
rs57251705	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs60517461	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6593292	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66528253	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6943341	0.87[ASN][1000 genomes]
rs6954499	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6955423	0.89[EUR][1000 genomes]
rs6973917	0.83[EUR][1000 genomes]
rs73132854	0.87[ASN][1000 genomes]
rs73132897	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs73360358	0.91[ASN][1000 genomes]
rs73360359	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7776550	0.87[EUR][1000 genomes]
rs7800001	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7811755	0.89[EUR][1000 genomes]
rs9642405	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	nsv1019400	chr7:55709827-56094540	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	nsv888064	chr7:55831721-56104539	Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers 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	39 gene(s)	inside rSNPs	diseases
10	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
11	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
12	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
13	nsv1034826	chr7:55962159-56092835	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats 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	27 gene(s)	inside rSNPs	diseases
14	nsv1033225	chr7:55962159-56094540	Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
15	nsv1017793	chr7:56051267-56098030	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6593294	CHCHD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56033200-56081400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr7:56033800-56065800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr7:56039200-56081600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr7:56045000-56067400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr7:56045200-56068200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:56045400-56067000	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr7:56045400-56067000	Strong transcription	Liver	Liver
8	chr7:56045400-56067200	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr7:56045400-56067400	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr7:56045600-56066600	Strong transcription	Fetal Stomach	stomach
11	chr7:56045600-56067400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr7:56045600-56067400	Strong transcription	Fetal Intestine Large	intestine
13	chr7:56045800-56066800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr7:56045800-56068000	Strong transcription	Fetal Muscle Trunk	muscle
15	chr7:56046200-56067200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr7:56046400-56065800	Strong transcription	Fetal Muscle Leg	muscle
17	chr7:56046400-56068200	Strong transcription	Skeletal Muscle Female	skeletal muscle
18	chr7:56047000-56068400	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr7:56049200-56067000	Weak transcription	Fetal Heart	heart
20	chr7:56049200-56101600	Weak transcription	Small Intestine	intestine
21	chr7:56049800-56066400	Weak transcription	K562	blood
22	chr7:56050000-56086600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr7:56051400-56086800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr7:56051600-56064000	Weak transcription	HepG2	liver
25	chr7:56051800-56077000	Weak transcription	NHEK	skin
26	chr7:56052800-56064200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr7:56053000-56074200	Weak transcription	Hela-S3	cervix
28	chr7:56053000-56078200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr7:56053400-56066200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr7:56054000-56064600	Weak transcription	Osteobl	bone
31	chr7:56055200-56068600	Strong transcription	Left Ventricle	heart
32	chr7:56055800-56066200	Strong transcription	Ovary	ovary
33	chr7:56057000-56067400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr7:56058400-56067200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr7:56058400-56068400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr7:56058400-56077800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr7:56058600-56066800	Strong transcription	Right Ventricle	heart
38	chr7:56058600-56068200	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr7:56058800-56067200	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr7:56058800-56067200	Strong transcription	Skeletal Muscle Male	skeletal muscle
41	chr7:56058800-56068400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr7:56059000-56067000	Strong transcription	Dnd41	blood
43	chr7:56059200-56065600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr7:56059200-56067200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr7:56059200-56068400	Strong transcription	Duodenum Mucosa	Duodenum
46	chr7:56059800-56066800	Strong transcription	Brain Germinal Matrix	brain
47	chr7:56059800-56067000	Strong transcription	Lung	lung
48	chr7:56059800-56068200	Strong transcription	Adipose Nuclei	Adipose
49	chr7:56059800-56068400	Strong transcription	Primary T cells from cord blood	blood
50	chr7:56059800-56068400	Strong transcription	Fetal Brain Female	brain

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