Variant report

Variant	rs1894834
Chromosome Location	chr7:56177066-56177067
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:56177023-56177073	SK-N-SH	brain:	n/a
2	chr7:56177023-56177073	HEEpiC	esophagus:	n/a
3	chr7:56177023-56177073	T-47D	breast:	n/a
4	chr7:56177023-56177073	HCF	heart:	n/a
5	chr7:56177023-56177073	PrEC	prostate:	n/a
6	chr7:56177023-56177073	U87	brain:	n/a
7	chr7:56177023-56177073	AG10803	skin:	n/a
8	chr7:56177023-56177073	AoSMC	blood vessel:	n/a
9	chr7:56177023-56177073	H1-hESC	embryonic stem cell:	embryo
10	chr7:56177023-56177073	NH-A	brain:	n/a
11	chr7:56177023-56177073	MCF10A-Er-Src	breast:	n/a
12	chr7:56177023-56177073	Hela-S3	cervix:	n/a
13	chr7:56177023-56177073	GM12892	blood:	n/a
14	chr7:56177023-56177073	PANC-1	pancreas:	n/a
15	chr7:56177023-56177073	HEK293	kidney:	embryo
16	chr7:56177023-56177073	GM12878	blood:	n/a
17	chr7:56177023-56177073	MCF-7	breast:	n/a
18	chr7:56177023-56177073	Caco-2	colon:	n/a
19	chr7:56177023-56177073	AG04450	lung:	fetal
20	chr7:56177023-56177073	A549	lung:	n/a
21	chr7:56177023-56177073	AG09309	skin:	n/a
22	chr7:56177023-56177073	LNCaP	prostate:	n/a
23	chr7:56177023-56177073	HPAEpiC	pulmonary alveolar:	n/a
24	chr7:56177023-56177073	NHDF-neo	bronchial:	n/a
25	chr7:56177023-56177073	SAEC	small airway:	n/a
26	chr7:56177023-56177073	NB4	blood:	n/a
27	chr7:56177023-56177073	HRPEpiC	eye:	n/a
28	chr7:56177023-56177073	HCPEpiC	choroid plexus:	n/a
29	chr7:56177023-56177073	HCM	heart:	n/a
30	chr7:56177023-56177073	BE2_C	brain:	n/a
31	chr7:56177023-56177073	Jurkat	blood:	n/a
32	chr7:56177023-56177073	HMEC	breast:	n/a
33	chr7:56177023-56177073	SK-N-SH_RA	brain:	n/a
34	chr7:56177023-56177073	IMR90	lung:	fetal
35	chr7:56177023-56177073	AG04449	skin:	fetal
36	chr7:56177023-56177073	AG09319	gingival:	n/a
37	chr7:56177023-56177073	HNPCEpiC	eye:	n/a
38	chr7:56177023-56177073	SKMC	muscle:	n/a
39	chr7:56177023-56177073	HIPEpiC	eye:	n/a
40	chr7:56177023-56177073	ovcar-3	ovarian:	n/a
41	chr7:56177023-56177073	RPTEC	kidney:	n/a
42	chr7:56177023-56177073	ProgFib	skin:	n/a
43	chr7:56177023-56177073	HCT-116	colon:	n/a
44	chr7:56177023-56177073	Hepatocyte	liver:	n/a
45	chr7:56177023-56177073	HepG2	liver:	n/a
46	chr7:56177023-56177073	NHBE	bronchial:	n/a
47	chr7:56177023-56177073	GM19239	blood:	n/a
48	chr7:56177023-56177073	K562	blood:	n/a
49	chr7:56177023-56177073	CMK	blood:	n/a
50	chr7:56177023-56177073	HL-60	blood:	n/a

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:56173545..56176378-chr7:56176611..56178258,2	K562	blood:

No data

Variant related genes	Relation type
CHCHD2	CpG island
ENSG00000106153	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10043	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1064337	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11238392	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11238393	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11238395	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11764629	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11765364	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11772545	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12535749	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12535872	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12538444	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1894833	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2002693	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2080141	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2538048	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2908546	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2908547	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2908548	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2965455	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4294145	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs55697950	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55863006	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56389944	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56401951	0.88[ASN][1000 genomes]
rs62457279	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62457281	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62457282	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62457284	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62457287	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62457288	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62457289	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62457291	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6951202	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6955663	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6965614	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73140771	0.86[AMR][1000 genomes]
rs7801405	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7808729	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7811889	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs816407	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs816410	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8406	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9649860	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
3	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
4	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
5	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
6	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
7	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
8	nsv1034712	chr7:56146885-56605592	Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
9	nsv538861	chr7:56146885-56605592	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
10	nsv526294	chr7:56171489-56622630	Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
11	nsv1016771	chr7:56174828-56643856	Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
12	nsv538862	chr7:56174828-56643856	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1894834	CHCHD2	Cis_1M	lymphoblastoid	RTeQTL
rs1894834	LOC146325	trans	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56174200-56183600	Weak transcription	Gastric	stomach
2	chr7:56175200-56183400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr7:56176200-56178400	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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