Variant report

Variant	rs10255049
Chromosome Location	chr7:56121304-56121305
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:56117687-56123706	K562	blood:	n/a	n/a
2	POLR2A	chr7:56120891-56122135	GM12892	blood:	n/a	n/a
3	POLR2A	chr7:56120847-56122610	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAFK	chr7:56121018-56121473	IMR90	lung:	n/a	chr7:56121273-56121288
5	POLR2A	chr7:56120765-56123238	K562	blood:	n/a	n/a
6	POLR2A	chr7:56120570-56122744	PFSK-1	brain:	n/a	n/a
7	MAFF	chr7:56121071-56121466	HepG2	liver:	n/a	chr7:56121272-56121290
8	POLR2A	chr7:56121058-56121409	ECC-1	luminal epithelium:	n/a	n/a
9	POLR2A	chr7:56117608-56122645	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr7:56120880-56122484	HepG2	liver:	n/a	n/a
11	MAFK	chr7:56120849-56121806	K562	blood:	n/a	chr7:56121273-56121288
12	POLR2A	chr7:56120905-56122391	GM12878	blood:	n/a	n/a
13	POLR2A	chr7:56120539-56122029	PANC-1	pancreas:	n/a	n/a
14	MAFK	chr7:56121096-56121466	HepG2	liver:	n/a	chr7:56121273-56121288
15	POLR2A	chr7:56121019-56121508	GM12892	blood:	n/a	n/a
16	POLR2A	chr7:56121102-56121415	MCF-7	breast:	n/a	n/a
17	MAFF	chr7:56120942-56121762	K562	blood:	n/a	chr7:56121272-56121290
18	POLR2A	chr7:56120954-56121426	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr7:56121011-56121487	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr7:56120491-56122456	PANC-1	pancreas:	n/a	n/a
21	POLR2A	chr7:56117859-56122614	K562	blood:	n/a	n/a
22	POLR2A	chr7:56121060-56121493	K562	blood:	n/a	n/a
23	POLR2A	chr7:56121040-56121437	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr7:56120622-56122531	K562	blood:	n/a	n/a
25	MAFK	chr7:56121083-56121458	Hela-S3	cervix:	n/a	chr7:56121273-56121288
26	POLR2A	chr7:56117844-56122283	PFSK-1	brain:	n/a	n/a
27	POLR2A	chr7:56117697-56122605	GM12891	blood:	n/a	n/a
28	POLR2A	chr7:56117565-56122648	MCF10A-Er-Src	breast:	n/a	n/a
29	MAFK	chr7:56121060-56121441	H1-hESC	embryonic stem cell:	n/a	chr7:56121273-56121288
30	POLR2A	chr7:56121011-56122559	HepG2	liver:	n/a	n/a
31	POLR2A	chr7:56117650-56122140	SK-N-MC	brain:	n/a	n/a
32	MAFK	chr7:56121091-56121470	HepG2	liver:	n/a	chr7:56121273-56121288
33	POLR2A	chr7:56120867-56121475	HepG2	liver:	n/a	n/a
34	POLR2A	chr7:56120995-56121481	GM12878	blood:	n/a	n/a
35	POLR2A	chr7:56121217-56121380	K562	blood:	n/a	n/a
36	POLR2A	chr7:56121068-56121431	H1-hESC	embryonic stem cell:	n/a	n/a
37	BHLHE40	chr7:56120874-56121461	K562	blood:	n/a	n/a
38	POLR2A	chr7:56117529-56122526	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:56119419..56122353-chr8:107669214..107670843,2	MCF-7	breast:
2	chr7:56117123..56123487-chr7:56128716..56133468,11	MCF-7	breast:
3	chr7:56100273..56103332-chr7:56118092..56121325,5	MCF-7	breast:

Variant related genes	Relation type
CCT6A	TF binding region
ENSG00000206603	TF binding region
PSPH	TF binding region
ENSG00000253582	Chromatin interaction
ENSG00000164830	Chromatin interaction
ENSG00000146733	Chromatin interaction
ENSG00000129103	Chromatin interaction
ENSG00000146731	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11238394	0.88[ASN][1000 genomes]
rs11771788	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11773374	0.85[ASN][1000 genomes]
rs11773453	0.84[ASN][1000 genomes]
rs12669623	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13234899	0.87[ASN][1000 genomes]
rs2230197	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2908543	0.84[ASN][1000 genomes]
rs2908544	0.84[ASN][1000 genomes]
rs2908545	0.84[ASN][1000 genomes]
rs2908550	0.84[ASN][1000 genomes]
rs3735665	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4049337	0.84[AMR][1000 genomes]
rs4948104	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4948106	0.86[ASN][1000 genomes]
rs6945795	0.90[ASN][1000 genomes]
rs6954546	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6958480	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6966609	0.84[AMR][1000 genomes]
rs7783339	0.90[ASN][1000 genomes]
rs7793921	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7801467	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7811270	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs816408	0.84[ASN][1000 genomes]
rs816409	0.84[ASN][1000 genomes]
rs816411	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	esv3425362	chr7:56118483-56121331	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10255049	CHCHD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56119800-56121400	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr7:56120000-56122400	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
3	chr7:56120200-56121400	Transcr. at gene 5' and 3'	NHEK	skin
4	chr7:56120200-56121600	Transcr. at gene 5' and 3'	Hela-S3	cervix
5	chr7:56120200-56122000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr7:56120200-56124000	Weak transcription	Spleen	Spleen
7	chr7:56120200-56125600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr7:56120200-56131200	Weak transcription	Aorta	Aorta
9	chr7:56120400-56121400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr7:56120400-56121400	Enhancers	Pancreas	Pancrea
11	chr7:56120400-56121400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
12	chr7:56120400-56121600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
13	chr7:56120400-56121800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr7:56120400-56122400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr7:56120400-56123000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr7:56120400-56123000	Weak transcription	Ovary	ovary
17	chr7:56120400-56124000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr7:56120400-56124000	Weak transcription	Gastric	stomach
19	chr7:56120600-56121400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr7:56120600-56121400	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
21	chr7:56120600-56121400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr7:56120600-56121400	Genic enhancers	Primary T cells fromperipheralblood	blood
23	chr7:56120600-56121400	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
24	chr7:56120600-56121400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr7:56120600-56121400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr7:56120600-56121400	Genic enhancers	Fetal Muscle Trunk	muscle
27	chr7:56120600-56121400	Genic enhancers	Placenta	Placenta
28	chr7:56120600-56121400	Genic enhancers	Left Ventricle	heart
29	chr7:56120600-56121400	Genic enhancers	Lung	lung
30	chr7:56120600-56121400	Genic enhancers	Sigmoid Colon	Sigmoid Colon
31	chr7:56120600-56121400	Transcr. at gene 5' and 3'	HepG2	liver
32	chr7:56120600-56121600	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr7:56120600-56121600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr7:56120600-56121600	Enhancers	Pancreatic Islets	Pancreatic Islet
35	chr7:56120600-56122000	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
36	chr7:56120600-56122000	Genic enhancers	Primary T cells from cord blood	blood
37	chr7:56120600-56122000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
38	chr7:56120600-56122000	Genic enhancers	NHDF-Ad	bronchial
39	chr7:56120600-56122600	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr7:56120600-56123600	Transcr. at gene 5' and 3'	A549	lung
41	chr7:56120600-56131000	Strong transcription	Adipose Nuclei	Adipose
42	chr7:56120800-56121400	Genic enhancers	H1 Cell Line	embryonic stem cell
43	chr7:56120800-56121400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr7:56120800-56121400	Genic enhancers	H9 Cell Line	embryonic stem cell
45	chr7:56120800-56121400	Genic enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr7:56120800-56121400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr7:56120800-56121400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr7:56120800-56121400	Genic enhancers	Fetal Kidney	kidney
49	chr7:56120800-56121400	Genic enhancers	Fetal Stomach	stomach
50	chr7:56120800-56121400	Weak transcription	Rectal Mucosa Donor 29	rectum

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