Variant report

Variant	rs6593296
Chromosome Location	chr7:56118293-56118294
allele	C/T
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	chr7:56117567-56120230	Raji	blood:	n/a	n/a
3	CTCF	chr7:56118280-56118510	NHDF-neo	bronchial:	n/a	n/a
4	POLR2A	chr7:56117946-56118457	Hela-S3	cervix:	n/a	n/a
5	MYC	chr7:56118137-56120255	K562	blood:	n/a	chr7:56118751-56118766 chr7:56118751-56118764 chr7:56118751-56118764 chr7:56118752-56118763 chr7:56118753-56118762 chr7:56118753-56118763 chr7:56118751-56118764 chr7:56118755-56118762 chr7:56118748-56118767 chr7:56119760-56119770 chr7:56118752-56118763
6	CTCF	chr7:56118240-56118390	AG10803	skin:	n/a	n/a
7	GATA1	chr7:56118200-56120092	PBDE	blood:	n/a	chr7:56118266-56118275
8	STAT3	chr7:56118132-56118487	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr7:56117590-56120711	K562	blood:	n/a	n/a
10	RPC155	chr7:56117776-56118523	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr7:56118022-56120418	K562	blood:	n/a	n/a
12	CEBPB	chr7:56118117-56118454	A549	lung:	n/a	n/a
13	HEY1	chr7:56117919-56118458	K562	blood:	n/a	n/a
14	POLR2A	chr7:56118145-56118374	H1-hESC	embryonic stem cell:	n/a	n/a
15	TBP	chr7:56118154-56118522	Hela-S3	cervix:	n/a	n/a
16	TAF1	chr7:56118115-56118415	Hela-S3	cervix:	n/a	n/a
17	TBL1XR1	chr7:56118076-56118382	K562	blood:	n/a	n/a
18	MYC	chr7:56118135-56119670	MCF10A-Er-Src	breast:	n/a	chr7:56118751-56118766 chr7:56118751-56118764 chr7:56118751-56118764 chr7:56118752-56118763 chr7:56118753-56118762 chr7:56118753-56118763 chr7:56118751-56118764 chr7:56118755-56118762 chr7:56118748-56118767 chr7:56118752-56118763
19	POLR2A	chr7:56118044-56118425	HCT-116	colon:	n/a	n/a
20	CEBPB	chr7:56118143-56118478	K562	blood:	n/a	n/a
21	POLR2A	chr7:56117871-56118389	K562	blood:	n/a	n/a
22	CTCF	chr7:56118260-56118410	HPAF	blood vessel:	n/a	n/a
23	POLR2A	chr7:56117608-56122645	MCF10A-Er-Src	breast:	n/a	n/a
24	POLR2A	chr7:56117700-56118540	GM12892	blood:	n/a	n/a
25	POLR2A	chr7:56118112-56118489	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr7:56118038-56118507	Hela-S3	cervix:	n/a	n/a
27	MYC	chr7:56118149-56120309	NB4	blood:	n/a	chr7:56118751-56118766 chr7:56118751-56118764 chr7:56118751-56118764 chr7:56118752-56118763 chr7:56118753-56118762 chr7:56118753-56118763 chr7:56118751-56118764 chr7:56118755-56118762 chr7:56118748-56118767 chr7:56119760-56119770 chr7:56118752-56118763
28	POLR2A	chr7:56117595-56120499	PANC-1	pancreas:	n/a	n/a
29	STAT3	chr7:56118237-56118438	MCF10A-Er-Src	breast:	n/a	n/a
30	POLR2A	chr7:56118218-56119986	PFSK-1	brain:	n/a	n/a
31	CTCF	chr7:56118240-56118390	GM12873	blood:	n/a	n/a
32	POLR2A	chr7:56117958-56118524	GM12892	blood:	n/a	n/a
33	POLR2A	chr7:56118102-56119915	K562	blood:	n/a	n/a
34	ARID3A	chr7:56117818-56118583	K562	blood:	n/a	n/a
35	POLR2A	chr7:56117734-56118596	GM12878	blood:	n/a	n/a
36	POLR2A	chr7:56117972-56120261	HUVEC	blood vessel:	n/a	n/a
37	CTCF	chr7:56118216-56118486	GM12878	blood:	n/a	n/a
38	MYC	chr7:56118140-56119899	K562	blood:	n/a	chr7:56118751-56118766 chr7:56118751-56118764 chr7:56118751-56118764 chr7:56118752-56118763 chr7:56118753-56118762 chr7:56118753-56118763 chr7:56118751-56118764 chr7:56118755-56118762 chr7:56118748-56118767 chr7:56119760-56119770 chr7:56118752-56118763
39	FOS	chr7:56117884-56118499	MCF10A-Er-Src	breast:	n/a	chr7:56118265-56118273 chr7:56118266-56118273
40	POLR2A	chr7:56118095-56118416	K562	blood:	n/a	n/a
41	POLR2A	chr7:56117811-56118564	GM12892	blood:	n/a	n/a
42	POLR2A	chr7:56117840-56118492	GM12891	blood:	n/a	n/a
43	POLR2A	chr7:56117903-56118384	ECC-1	luminal epithelium:	n/a	n/a
44	POLR2A	chr7:56117587-56119887	HUVEC	blood vessel:	n/a	n/a
45	POLR2A	chr7:56117175-56121009	HepG2	liver:	n/a	n/a
46	MAX	chr7:56118092-56120303	NB4	blood:	n/a	chr7:56118751-56118766 chr7:56118751-56118764 chr7:56118751-56118764 chr7:56118752-56118763 chr7:56118753-56118762 chr7:56118753-56118763 chr7:56118751-56118764 chr7:56118755-56118762 chr7:56118748-56118767 chr7:56119760-56119770 chr7:56118752-56118763
47	MAX	chr7:56118136-56120044	Hela-S3	cervix:	n/a	chr7:56118751-56118766 chr7:56118751-56118764 chr7:56118751-56118764 chr7:56118752-56118763 chr7:56118753-56118762 chr7:56118753-56118763 chr7:56118751-56118764 chr7:56118755-56118762 chr7:56118748-56118767 chr7:56119760-56119770 chr7:56118752-56118763
48	ARID3A	chr7:56118169-56118554	HepG2	liver:	n/a	n/a
49	CTCF	chr7:56118260-56118410	HMF	breast:	n/a	n/a
50	FOS	chr7:56118077-56118479	MCF10A-Er-Src	breast:	n/a	chr7:56118265-56118273 chr7:56118266-56118273

No.	Distal block	Cell Line	Cell type
1	chr7:56100362..56103278-chr7:56116659..56119395,4	K562	blood:
2	chr7:56117578..56119708-chr7:56126304..56127920,2	MCF-7	breast:
3	chr7:56031349..56032951-chr7:56117963..56119524,2	K562	blood:
4	chr7:56029925..56033959-chr7:56116899..56121286,8	MCF-7	breast:
5	chr7:56117123..56123487-chr7:56128716..56133468,11	MCF-7	breast:
6	chr7:56031975..56033890-chr7:56117908..56119685,2	MCF-7	breast:
7	chr7:56100095..56103801-chr7:56117179..56120388,5	K562	blood:
8	chr7:56100273..56103332-chr7:56118092..56121325,5	MCF-7	breast:
9	chr7:56031349..56034408-chr7:56116793..56119463,3	K562	blood:

Variant related genes	Relation type
CCT6A	TF binding region
ENSG00000206603	TF binding region
ENSG00000129103	Chromatin interaction
ENSG00000146731	Chromatin interaction
ENSG00000146733	Chromatin interaction
ENSG00000146729	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1057603	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11765364	0.83[CEU][hapmap];0.83[MKK][hapmap]
rs13226516	0.89[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62457265	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62457285	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6965614	0.85[YRI][hapmap]
rs7808729	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs6593296	LOC146325	trans	lymphoblastoid	RTeQTL
rs6593296	ZNF713	cis	cerebellum	SCAN
rs6593296	CHCHD2	cis	multi-tissue	Pritchard
rs6593296	CHCHD2	Cis_1M	lymphoblastoid	RTeQTL
rs6593296	CHCHD2	cis	lymphoblastoid	GTEx
rs6593296	LOC645317	trans	multi-tissue	Pritchard
rs6593296	CHCHD2	cis	parietal	SCAN
rs6593296	GBAS	cis	parietal	SCAN
rs6593296	CHCHD2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56108800-56118600	Weak transcription	Aorta	Aorta
2	chr7:56116000-56118400	Enhancers	Fetal Heart	heart
3	chr7:56117400-56118400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr7:56117600-56118400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr7:56117600-56118400	Enhancers	Fetal Muscle Trunk	muscle
6	chr7:56117600-56118400	Flanking Active TSS	Dnd41	blood
7	chr7:56117600-56118400	Flanking Active TSS	GM12878-XiMat	blood
8	chr7:56117600-56118400	Flanking Active TSS	Hela-S3	cervix
9	chr7:56117600-56118600	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr7:56117600-56118600	Enhancers	Esophagus	oesophagus
11	chr7:56117600-56118600	Enhancers	Gastric	stomach
12	chr7:56117600-56118600	Enhancers	Lung	lung
13	chr7:56117600-56118600	Enhancers	Placenta Amnion	Placenta Amnion
14	chr7:56117600-56118600	Enhancers	Spleen	Spleen
15	chr7:56117600-56118800	Enhancers	Fetal Brain Male	brain
16	chr7:56117600-56120000	Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr7:56117800-56118400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr7:56117800-56118400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr7:56117800-56118400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr7:56117800-56118400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
21	chr7:56117800-56118400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr7:56117800-56118400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr7:56117800-56118400	Enhancers	Brain Substantia Nigra	brain
24	chr7:56117800-56118400	Flanking Active TSS	Duodenum Mucosa	Duodenum
25	chr7:56117800-56118400	Enhancers	Placenta	Placenta
26	chr7:56117800-56118400	Weak transcription	Stomach Mucosa	stomach
27	chr7:56117800-56118400	Enhancers	Monocytes-CD14+_RO01746	blood
28	chr7:56117800-56118400	Flanking Active TSS	NHDF-Ad	bronchial
29	chr7:56117800-56118600	Enhancers	Primary T cells fromperipheralblood	blood
30	chr7:56117800-56118600	Enhancers	Primary hematopoietic stem cells	blood
31	chr7:56117800-56118600	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr7:56117800-56118600	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr7:56117800-56118600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr7:56117800-56118600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
35	chr7:56117800-56118600	Flanking Active TSS	Brain Cingulate Gyrus	brain
36	chr7:56117800-56118600	Flanking Active TSS	Colon Smooth Muscle	Colon
37	chr7:56117800-56118600	Flanking Active TSS	Fetal Intestine Small	intestine
38	chr7:56117800-56118600	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr7:56117800-56118600	Weak transcription	Small Intestine	intestine
40	chr7:56117800-56118800	Flanking Active TSS	NH-A	brain
41	chr7:56117800-56119000	Flanking Active TSS	HUVEC	blood vessel
42	chr7:56117800-56119200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr7:56117800-56119200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr7:56117800-56119200	Flanking Active TSS	Adipose Nuclei	Adipose
45	chr7:56117800-56120200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr7:56117800-56120200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr7:56117800-56120600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr7:56117800-56120600	Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr7:56117800-56120600	Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr7:56118000-56118400	Flanking Active TSS	H1 Cell Line	embryonic stem cell

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