Variant report

Variant	rs4948108
Chromosome Location	chr7:56173628-56173629
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:56047807..56050319-chr7:56171893..56174174,2	K562	blood:
2	chr7:56171801..56173788-chr7:56307425..56310338,2	K562	blood:
3	chr7:56173528..56175860-chr7:56295526..56297795,2	K562	blood:

Variant related genes	Relation type
ENSG00000227491	Chromatin interaction
ENSG00000146729	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs17172508	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17664478	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap]
rs2192262	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3966180	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4443615	0.82[EUR][1000 genomes]
rs4495378	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs4948095	0.82[EUR][1000 genomes]
rs4948098	1.00[ASN][1000 genomes]
rs4948103	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4948107	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58571234	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59193297	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59852874	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6593298	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66485869	1.00[ASN][1000 genomes]
rs66741911	1.00[ASN][1000 genomes]
rs67818657	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6947109	1.00[ASN][1000 genomes]
rs6954669	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73132395	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73132398	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73134793	0.82[EUR][1000 genomes]
rs73134796	0.82[EUR][1000 genomes]
rs73135709	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73138732	1.00[ASN][1000 genomes]
rs73138736	1.00[ASN][1000 genomes]
rs73138750	1.00[ASN][1000 genomes]
rs73140745	1.00[ASN][1000 genomes]
rs73140778	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7779821	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784730	1.00[ASN][1000 genomes]
rs7791221	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7806994	0.99[EUR][1000 genomes]
rs7808487	1.00[ASN][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	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
11	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
12	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
13	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4948108	CHCHD2	cis	multi-tissue	Pritchard
rs4948108	CHCHD2	cis	Whole Blood	GTEx
rs4948108	LOC645345	trans	multi-tissue	Pritchard
rs4948108	CHCHD2	cis	Esophagus Mucosa	GTEx
rs4948108	ZNF713	cis	cerebellum	SCAN
rs4948108	CHCHD2	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56172200-56174800	Active TSS	GM12878-XiMat	blood
2	chr7:56172200-56175000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr7:56172600-56174800	Active TSS	Psoas Muscle	Psoas
4	chr7:56172600-56175000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr7:56172600-56175000	Active TSS	HSMM	muscle
6	chr7:56172800-56173800	Flanking Active TSS	Primary T cells from cord blood	blood
7	chr7:56172800-56173800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr7:56172800-56174000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr7:56172800-56174600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr7:56172800-56174800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr7:56172800-56174800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr7:56172800-56174800	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr7:56172800-56174800	Active TSS	Muscle Satellite Cultured Cells	--
14	chr7:56172800-56174800	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr7:56172800-56174800	Active TSS	Rectal Smooth Muscle	rectum
16	chr7:56172800-56174800	Active TSS	HMEC	breast
17	chr7:56172800-56175000	Active TSS	NHLF	lung
18	chr7:56173000-56173800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
19	chr7:56173000-56173800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
20	chr7:56173000-56173800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
21	chr7:56173000-56173800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
22	chr7:56173000-56174200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
23	chr7:56173000-56174600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr7:56173000-56174600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr7:56173000-56174600	Active TSS	Ovary	ovary
26	chr7:56173000-56174800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr7:56173000-56174800	Active TSS	HUES6 Cell Line	embryonic stem cell
28	chr7:56173000-56174800	Active TSS	HUES64 Cell Line	embryonic stem cell
29	chr7:56173000-56174800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr7:56173000-56174800	Active TSS	Right Ventricle	heart
31	chr7:56173000-56174800	Active TSS	Thymus	Thymus
32	chr7:56173000-56175000	Active TSS	iPS-18 Cell Line	embryonic stem cell
33	chr7:56173000-56175000	Active TSS	Right Atrium	heart
34	chr7:56173000-56175200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
35	chr7:56173200-56173800	Flanking Active TSS	Primary hematopoietic stem cells	blood
36	chr7:56173200-56174000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
37	chr7:56173200-56174200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr7:56173200-56174200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr7:56173200-56174200	Active TSS	Gastric	stomach
40	chr7:56173200-56174400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr7:56173200-56174600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
42	chr7:56173200-56174600	Active TSS	H1 Cell Line	embryonic stem cell
43	chr7:56173200-56174600	Active TSS	H9 Cell Line	embryonic stem cell
44	chr7:56173200-56174600	Active TSS	HUES48 Cell Line	embryonic stem cell
45	chr7:56173200-56174600	Active TSS	iPS-15b Cell Line	embryonic stem cell
46	chr7:56173200-56174600	Active TSS	Esophagus	oesophagus
47	chr7:56173200-56174600	Active TSS	Fetal Kidney	kidney
48	chr7:56173200-56174600	Active TSS	Left Ventricle	heart
49	chr7:56173200-56174600	Active TSS	Stomach Mucosa	stomach
50	chr7:56173200-56174800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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