Variant report

Variant	rs872294
Chromosome Location	chr7:55956468-55956469
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr7:55955568-55956879	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:55954730..55957503-chr7:55957932..55960617,3	K562	blood:
2	chr7:55953245..55956784-chr7:55957115..55962697,6	MCF-7	breast:
3	chr7:55954730..55957550-chr7:55957932..55963672,5	K562	blood:

Variant related genes	Relation type
RN7SL64P	TF binding region
ENSG00000265676	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs17172508	0.93[CEU][hapmap]
rs17664478	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4443615	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4495378	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4948095	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6964563	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73132850	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73132884	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73132888	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73134793	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs73134796	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs73138736	0.85[AFR][1000 genomes]
rs7776908	1.00[ASN][1000 genomes]
rs7791221	0.92[CEU][hapmap]
rs7810142	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs872294	CHCHD2	cis	Whole Blood	GTEx

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:55954400-55956600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr7:55954400-55956600	Active TSS	Brain Germinal Matrix	brain
3	chr7:55954800-55956600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr7:55955400-55961600	Weak transcription	Spleen	Spleen
5	chr7:55955400-56004200	Weak transcription	Gastric	stomach
6	chr7:55955800-55956600	Flanking Active TSS	Dnd41	blood
7	chr7:55955800-55973800	Weak transcription	Left Ventricle	heart
8	chr7:55955800-55975000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr7:55955800-55985800	Weak transcription	Esophagus	oesophagus
10	chr7:55956000-55956600	Enhancers	Fetal Heart	heart
11	chr7:55956000-55956600	Enhancers	Right Ventricle	heart
12	chr7:55956000-55956800	Enhancers	Primary T cells fromperipheralblood	blood
13	chr7:55956000-55974200	Weak transcription	Aorta	Aorta
14	chr7:55956000-55979600	Weak transcription	Psoas Muscle	Psoas
15	chr7:55956200-55956600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr7:55956200-55956600	Enhancers	Brain Cingulate Gyrus	brain
17	chr7:55956200-55956600	Enhancers	Fetal Brain Male	brain
18	chr7:55956200-55956800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr7:55956200-55958600	Weak transcription	NH-A	brain
20	chr7:55956200-55961600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr7:55956200-55961600	Weak transcription	Fetal Intestine Small	intestine
22	chr7:55956200-55962600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr7:55956200-55967600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr7:55956200-55973800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr7:55956200-55974000	Weak transcription	Ovary	ovary
26	chr7:55956200-55974200	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr7:55956200-55975200	Weak transcription	HSMMtube	muscle
28	chr7:55956200-55979400	Weak transcription	Primary T cells from cord blood	blood
29	chr7:55956200-55979600	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr7:55956200-55990800	Weak transcription	Thymus	Thymus
31	chr7:55956200-56002200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr7:55956400-55956600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr7:55956400-55956600	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr7:55956400-55956600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr7:55956400-55956600	Active TSS	Fetal Brain Female	brain
36	chr7:55956400-55956600	Enhancers	Fetal Muscle Trunk	muscle
37	chr7:55956400-55956600	Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr7:55956400-55956800	Enhancers	Hela-S3	cervix
39	chr7:55956400-55957600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr7:55956400-55959400	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr7:55956400-55960200	Weak transcription	Fetal Stomach	stomach
42	chr7:55956400-55961200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr7:55956400-55961600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr7:55956400-55961600	Weak transcription	Right Atrium	heart
45	chr7:55956400-55961600	Weak transcription	HepG2	liver
46	chr7:55956400-55963400	Weak transcription	Primary hematopoietic stem cells	blood
47	chr7:55956400-55965200	Weak transcription	Fetal Lung	lung
48	chr7:55956400-55965400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr7:55956400-55965800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr7:55956400-55966000	Weak transcription	Fetal Muscle Leg	muscle

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