Variant report

Variant	rs12669623
Chromosome Location	chr7:56139179-56139180
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	chr7:56132081..56135205-chr7:56137628..56140599,3	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10081373	0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10255049	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11238389	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11771788	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12537943	0.91[ASN][1000 genomes]
rs13240915	0.88[ASN][1000 genomes]
rs13241866	0.88[ASN][1000 genomes]
rs13244654	0.95[ASN][1000 genomes]
rs2002651	0.94[ASN][1000 genomes]
rs2016724	0.92[ASN][1000 genomes]
rs2230197	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2242508	0.93[ASN][1000 genomes]
rs2538047	0.89[ASN][1000 genomes]
rs3735665	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4049337	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4275190	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4947534	0.81[ASN][1000 genomes]
rs4948102	0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4948104	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62457261	0.80[ASN][1000 genomes]
rs6593297	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6954546	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6955423	0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6958480	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6966609	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6973917	0.82[ASN][1000 genomes]
rs6975311	0.82[ASN][1000 genomes]
rs766333	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7776550	0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7793921	0.85[AMR][1000 genomes]
rs7801467	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7811270	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7811755	0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9767946	0.95[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12669623	CHCHD2	Cis_1M	lymphoblastoid	RTeQTL

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	chr7:56132400-56141800	Weak transcription	Stomach Mucosa	stomach
3	chr7:56132400-56145400	Weak transcription	Spleen	Spleen
4	chr7:56133200-56140600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr7:56133200-56141800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr7:56133200-56141800	Weak transcription	HepG2	liver
7	chr7:56133200-56142000	Weak transcription	Esophagus	oesophagus
8	chr7:56133200-56142200	Weak transcription	Right Atrium	heart
9	chr7:56133200-56145600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr7:56133200-56146400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr7:56133200-56147000	Weak transcription	Fetal Brain Male	brain
12	chr7:56133200-56147000	Weak transcription	Psoas Muscle	Psoas
13	chr7:56133400-56144200	Weak transcription	Primary hematopoietic stem cells	blood
14	chr7:56133400-56145800	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr7:56133600-56141800	Weak transcription	HUVEC	blood vessel
16	chr7:56133600-56144200	Weak transcription	NHDF-Ad	bronchial
17	chr7:56133600-56145400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr7:56133800-56141800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr7:56133800-56142000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr7:56133800-56143200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr7:56134000-56141800	Weak transcription	NHLF	lung
22	chr7:56134000-56152000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr7:56134000-56167800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr7:56134200-56139600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr7:56134200-56167600	Weak transcription	Small Intestine	intestine
26	chr7:56134600-56139400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr7:56134600-56139600	Strong transcription	Dnd41	blood
28	chr7:56134600-56141200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr7:56134800-56139600	Strong transcription	Primary T cells from cord blood	blood
30	chr7:56134800-56141000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr7:56135000-56139200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr7:56135000-56141600	Strong transcription	Fetal Muscle Leg	muscle
33	chr7:56135000-56141800	Strong transcription	Fetal Intestine Small	intestine
34	chr7:56135000-56142600	Strong transcription	Fetal Stomach	stomach
35	chr7:56135400-56141000	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr7:56135800-56139200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr7:56135800-56139400	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr7:56135800-56141000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr7:56135800-56141800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr7:56136000-56139200	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr7:56136000-56139400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr7:56136000-56139400	Strong transcription	Fetal Intestine Large	intestine
43	chr7:56136000-56139400	Strong transcription	Fetal Thymus	thymus
44	chr7:56136000-56139600	Strong transcription	Fetal Muscle Trunk	muscle
45	chr7:56136000-56140000	Strong transcription	H1 Cell Line	embryonic stem cell
46	chr7:56136000-56141000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr7:56136000-56141000	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr7:56136000-56141000	Strong transcription	Liver	Liver
49	chr7:56136000-56141000	Strong transcription	Thymus	Thymus
50	chr7:56136000-56141200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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