Variant report

Variant	rs7801405
Chromosome Location	chr7:56082622-56082623
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10043	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1064337	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11238392	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11238393	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11238395	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11764629	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11765364	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11772545	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12535749	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12535872	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12538444	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1894833	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1894834	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2002693	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2080141	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2538048	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2908546	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2908547	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2908548	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2965455	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55634856	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55697950	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55863006	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56128104	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56207001	0.83[EUR][1000 genomes]
rs56351949	0.82[EUR][1000 genomes]
rs56389944	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62457279	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62457281	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62457282	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62457284	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62457287	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62457288	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62457289	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62457291	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6951202	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6955663	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6965614	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71015156	0.86[AFR][1000 genomes]
rs73140771	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7808729	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7811889	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs816407	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs816410	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8406	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9649860	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7801405	CHCHD2	Cis_1M	lymphoblastoid	RTeQTL
rs7801405	LOC146325	trans	lymphoblastoid	RTeQTL

Chromatin state (count:108 , 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	chr7:56050000-56086600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr7:56051400-56086800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:56060600-56099600	Weak transcription	HUVEC	blood vessel
5	chr7:56063400-56089600	Weak transcription	NHDF-Ad	bronchial
6	chr7:56063400-56096800	Weak transcription	NH-A	brain
7	chr7:56063600-56101000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr7:56063600-56101200	Weak transcription	NHLF	lung
9	chr7:56064400-56087200	Weak transcription	Aorta	Aorta
10	chr7:56064400-56087200	Weak transcription	Esophagus	oesophagus
11	chr7:56064400-56101400	Weak transcription	Gastric	stomach
12	chr7:56065000-56101400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr7:56065000-56101400	Weak transcription	Colonic Mucosa	Colon
14	chr7:56065400-56101400	Weak transcription	Fetal Brain Male	brain
15	chr7:56065800-56088400	Weak transcription	Fetal Kidney	kidney
16	chr7:56065800-56095800	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr7:56066200-56086600	Weak transcription	Ovary	ovary
18	chr7:56066600-56087400	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr7:56066800-56086000	Weak transcription	Brain Germinal Matrix	brain
20	chr7:56067000-56088600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr7:56067200-56087000	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr7:56067200-56101400	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr7:56067400-56087200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr7:56067400-56087600	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr7:56067400-56100800	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr7:56067800-56099600	Weak transcription	K562	blood
27	chr7:56068200-56086200	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr7:56068200-56087400	Weak transcription	Adipose Nuclei	Adipose
29	chr7:56068200-56101200	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr7:56068400-56087200	Weak transcription	Fetal Brain Female	brain
31	chr7:56072800-56087400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr7:56073000-56085800	Weak transcription	Right Ventricle	heart
33	chr7:56074400-56086400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr7:56075400-56101400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr7:56075800-56086600	Weak transcription	Hela-S3	cervix
36	chr7:56077200-56087200	Strong transcription	Fetal Intestine Small	intestine
37	chr7:56077600-56085600	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr7:56077600-56087200	Weak transcription	Pancreas	Pancrea
39	chr7:56077600-56089200	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr7:56077800-56083600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr7:56077800-56088000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr7:56077800-56099600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr7:56077800-56100600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr7:56078000-56083800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr7:56078000-56087200	Weak transcription	Rectal Smooth Muscle	rectum
46	chr7:56078000-56087200	Weak transcription	Stomach Smooth Muscle	stomach
47	chr7:56078000-56088200	Weak transcription	Brain Angular Gyrus	brain
48	chr7:56078200-56083200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr7:56078200-56083600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr7:56078200-56083800	Strong transcription	Fetal Muscle Trunk	muscle

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