Variant report

Variant	rs10250964
Chromosome Location	chr7:55998920-55998921
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10229446	0.86[ASN][1000 genomes]
rs10245725	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10252442	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10266902	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10271662	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10272406	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10435504	0.86[ASN][1000 genomes]
rs11765531	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11765577	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2135116	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28636652	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28678267	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28828764	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34016595	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35844144	0.87[ASN][1000 genomes]
rs4470984	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4535700	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4543497	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4689	0.86[ASN][1000 genomes]
rs4947533	0.83[ASN][1000 genomes]
rs4948096	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4948097	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4948099	0.84[ASN][1000 genomes]
rs57153841	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57251705	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60517461	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6593292	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6593294	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs66528253	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6943341	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6954499	0.84[ASN][1000 genomes]
rs73132854	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73132897	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73360358	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73360359	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7800001	0.83[ASN][1000 genomes]
rs9642405	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	nsv427782	chr7:55703073-56010314	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	nsv607034	chr7:55974028-56002247	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10250964	CHCHD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:55955400-56004200	Weak transcription	Gastric	stomach
2	chr7:55956200-56002200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr7:55975000-56002000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr7:55975800-56006800	Weak transcription	Fetal Kidney	kidney
5	chr7:55978800-55999400	Weak transcription	Placenta	Placenta
6	chr7:55980000-55999000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr7:55980000-56001400	Weak transcription	Spleen	Spleen
8	chr7:55980400-56004000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr7:55980600-55999400	Weak transcription	Psoas Muscle	Psoas
10	chr7:55980600-56001200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr7:55980600-56004200	Weak transcription	Right Ventricle	heart
12	chr7:55980800-55999400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr7:55982600-56006200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr7:55985800-55999600	Weak transcription	Dnd41	blood
15	chr7:55986600-56006800	Weak transcription	Fetal Brain Male	brain
16	chr7:55990400-56000200	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr7:55991400-56002200	Weak transcription	Aorta	Aorta
18	chr7:55993000-56004200	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr7:55993400-56002200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr7:55993400-56002400	Weak transcription	Primary T cells from cord blood	blood
21	chr7:55993600-55999400	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr7:55993600-56001400	Weak transcription	Brain Substantia Nigra	brain
23	chr7:55993600-56001400	Weak transcription	HSMMtube	muscle
24	chr7:55993800-55999400	Weak transcription	Thymus	Thymus
25	chr7:55994600-56000000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr7:55996000-55999400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr7:55996200-56002200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr7:55996200-56004000	Weak transcription	Brain Angular Gyrus	brain
29	chr7:55996400-56001400	Weak transcription	Brain Anterior Caudate	brain
30	chr7:55996400-56001400	Weak transcription	Fetal Lung	lung
31	chr7:55996400-56001400	Weak transcription	Ovary	ovary
32	chr7:55996600-56001400	Weak transcription	Brain Germinal Matrix	brain
33	chr7:55996600-56006800	Weak transcription	Fetal Heart	heart
34	chr7:55996800-55999200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr7:55996800-56004000	Weak transcription	Fetal Muscle Trunk	muscle
36	chr7:55997400-55999600	Strong transcription	Fetal Brain Female	brain
37	chr7:55998000-55999800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
38	chr7:55998200-56004000	Weak transcription	Stomach Smooth Muscle	stomach
39	chr7:55998400-55999400	Weak transcription	Liver	Liver
40	chr7:55998400-55999400	Weak transcription	Brain Hippocampus Middle	brain
41	chr7:55998400-55999400	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr7:55998400-55999400	Weak transcription	Pancreas	Pancrea
43	chr7:55998400-56002200	Weak transcription	Left Ventricle	heart
44	chr7:55998400-56004000	Weak transcription	Fetal Muscle Leg	muscle
45	chr7:55998600-55999400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr7:55998600-56001200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr7:55998800-55999800	Strong transcription	Fetal Stomach	stomach

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