Variant report

Variant	rs13240915
Chromosome Location	chr7:56090752-56090753
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10081373	0.90[ASN][1000 genomes]
rs10229446	0.85[CHB][hapmap];0.89[EUR][1000 genomes]
rs10435504	0.87[EUR][1000 genomes]
rs11238389	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11771788	0.84[ASN][1000 genomes]
rs12537943	0.80[ASN][1000 genomes]
rs12669623	0.88[ASN][1000 genomes]
rs13241866	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13244654	0.90[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs2002651	0.86[ASN][1000 genomes]
rs2016724	0.89[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs2230197	0.88[ASN][1000 genomes]
rs2242508	0.90[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs3735665	0.88[ASN][1000 genomes]
rs4275190	0.90[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4470984	0.80[CHB][hapmap];0.84[EUR][1000 genomes]
rs4535700	0.86[CHB][hapmap];0.85[EUR][1000 genomes]
rs4543497	0.85[CHB][hapmap];0.85[EUR][1000 genomes]
rs4689	0.85[CHB][hapmap];0.89[EUR][1000 genomes]
rs4947533	0.85[CHB][hapmap];0.89[EUR][1000 genomes]
rs4947534	0.94[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4948096	0.85[CHB][hapmap];0.87[EUR][1000 genomes]
rs4948097	0.87[EUR][1000 genomes]
rs4948099	0.91[EUR][1000 genomes]
rs4948102	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4948104	0.88[ASN][1000 genomes]
rs62457261	0.91[ASN][1000 genomes]
rs6593292	0.86[CHB][hapmap];0.84[EUR][1000 genomes]
rs6593294	0.89[EUR][1000 genomes]
rs6593297	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs6951810	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6954499	0.84[EUR][1000 genomes]
rs6954546	0.84[ASN][1000 genomes]
rs6955423	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6958480	0.90[ASN][1000 genomes]
rs6966609	0.84[ASN][1000 genomes]
rs6973917	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6975311	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs766333	0.89[ASN][1000 genomes]
rs7776550	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7800001	0.91[EUR][1000 genomes]
rs7801467	0.84[ASN][1000 genomes]
rs7811270	0.88[ASN][1000 genomes]
rs7811755	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9767946	0.84[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	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
16	nsv966929	chr7:56085012-56094574	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13240915	CHCHD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56049200-56101600	Weak transcription	Small Intestine	intestine
2	chr7:56060600-56099600	Weak transcription	HUVEC	blood vessel
3	chr7:56063400-56096800	Weak transcription	NH-A	brain
4	chr7:56063600-56101000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr7:56063600-56101200	Weak transcription	NHLF	lung
6	chr7:56064400-56101400	Weak transcription	Gastric	stomach
7	chr7:56065000-56101400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr7:56065000-56101400	Weak transcription	Colonic Mucosa	Colon
9	chr7:56065400-56101400	Weak transcription	Fetal Brain Male	brain
10	chr7:56065800-56095800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr7:56067200-56101400	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr7:56067400-56100800	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr7:56067800-56099600	Weak transcription	K562	blood
14	chr7:56068200-56101200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr7:56075400-56101400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr7:56077800-56099600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr7:56077800-56100600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr7:56078200-56091000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr7:56078200-56091200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr7:56078200-56099800	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr7:56078200-56101200	Weak transcription	Colon Smooth Muscle	Colon
22	chr7:56078400-56091200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr7:56078400-56094400	Weak transcription	HMEC	breast
24	chr7:56081600-56097000	Weak transcription	Placenta	Placenta
25	chr7:56082200-56101200	Weak transcription	Duodenum Mucosa	Duodenum
26	chr7:56082600-56101200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr7:56083200-56092800	Weak transcription	HSMM	muscle
28	chr7:56083600-56096800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr7:56085600-56094400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr7:56086000-56091000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr7:56086000-56100200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr7:56086400-56098400	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr7:56086800-56101200	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr7:56087400-56101400	Weak transcription	Brain Germinal Matrix	brain
35	chr7:56087600-56091200	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr7:56087600-56101200	Weak transcription	Stomach Smooth Muscle	stomach
37	chr7:56087600-56101400	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr7:56087800-56097200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr7:56087800-56101400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr7:56088000-56095000	Weak transcription	Brain Cingulate Gyrus	brain
41	chr7:56088000-56101400	Weak transcription	Esophagus	oesophagus
42	chr7:56088000-56101600	Weak transcription	Lung	lung
43	chr7:56088400-56093200	Strong transcription	Fetal Intestine Small	intestine
44	chr7:56088600-56091000	Strong transcription	Fetal Intestine Large	intestine
45	chr7:56088600-56091000	Strong transcription	HepG2	liver
46	chr7:56088600-56101600	Weak transcription	Spleen	Spleen
47	chr7:56088800-56095800	Weak transcription	Fetal Brain Female	brain
48	chr7:56088800-56096000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr7:56088800-56096600	Weak transcription	Thymus	Thymus
50	chr7:56088800-56096800	Weak transcription	Brain Hippocampus Middle	brain

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