Variant report

Variant	rs6593297
Chromosome Location	chr7:56122058-56122059
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:28)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:28 , 50 per page) page: 1

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	POLR2A	chr7:56120765-56123238	K562	blood:	n/a	n/a
5	POLR2A	chr7:56120570-56122744	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr7:56117608-56122645	MCF10A-Er-Src	breast:	n/a	n/a
7	HEY1	chr7:56121633-56122209	HepG2	liver:	n/a	n/a
8	POLR2A	chr7:56120880-56122484	HepG2	liver:	n/a	n/a
9	POLR2A	chr7:56120905-56122391	GM12878	blood:	n/a	n/a
10	NFATC1	chr7:56121612-56122129	GM12878	blood:	n/a	n/a
11	POLR2A	chr7:56120491-56122456	PANC-1	pancreas:	n/a	n/a
12	POLR2A	chr7:56121873-56122303	GM12878	blood:	n/a	n/a
13	POLR2A	chr7:56117859-56122614	K562	blood:	n/a	n/a
14	POLR2A	chr7:56121945-56122242	GM12892	blood:	n/a	n/a
15	POLR2A	chr7:56120622-56122531	K562	blood:	n/a	n/a
16	POLR2A	chr7:56117844-56122283	PFSK-1	brain:	n/a	n/a
17	POLR2A	chr7:56122034-56122179	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr7:56117697-56122605	GM12891	blood:	n/a	n/a
19	POLR2A	chr7:56117565-56122648	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr7:56121665-56122188	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr7:56121770-56122508	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr7:56121011-56122559	HepG2	liver:	n/a	n/a
23	POLR2A	chr7:56121721-56122092	HepG2	liver:	n/a	n/a
24	POLR2A	chr7:56117650-56122140	SK-N-MC	brain:	n/a	n/a
25	POLR2A	chr7:56121981-56122247	H1-hESC	embryonic stem cell:	n/a	n/a
26	TBL1XR1	chr7:56121703-56122108	K562	blood:	n/a	n/a
27	POLR2A	chr7:56121595-56122294	HepG2	liver:	n/a	n/a
28	POLR2A	chr7:56117529-56122526	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:56119419..56122353-chr8:107669214..107670843,2	MCF-7	breast:
2	chr7:56117123..56123487-chr7:56128716..56133468,11	MCF-7	breast:

No data

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

Extended variants
information (count: 54 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10081373	0.86[ASN][1000 genomes]
rs10229446	1.00[ASW][hapmap];0.80[MEX][hapmap];0.88[YRI][hapmap]
rs10245725	0.94[ASW][hapmap];0.80[YRI][hapmap]
rs10252442	0.94[ASW][hapmap];0.80[YRI][hapmap]
rs10271662	0.94[ASW][hapmap];0.84[YRI][hapmap]
rs10272406	0.83[YRI][hapmap]
rs10435504	0.87[YRI][hapmap]
rs11238394	0.81[CHB][hapmap]
rs11771788	0.83[AMR][1000 genomes]
rs12669623	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs13240915	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs13241866	0.90[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap]
rs13244654	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs2002651	0.82[ASN][1000 genomes]
rs2016724	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2135116	0.94[ASW][hapmap];0.80[YRI][hapmap]
rs2230197	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2242508	1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap]
rs28828764	0.94[ASW][hapmap];0.80[YRI][hapmap]
rs2908543	0.81[CHB][hapmap]
rs3735665	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4049337	0.85[AMR][1000 genomes]
rs4275190	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4470984	1.00[ASW][hapmap];0.80[MEX][hapmap];0.84[YRI][hapmap]
rs4535700	0.88[YRI][hapmap]
rs4543497	1.00[ASW][hapmap];0.80[MEX][hapmap];0.88[YRI][hapmap]
rs4689	1.00[ASW][hapmap];0.80[MEX][hapmap];0.88[YRI][hapmap]
rs4947533	1.00[ASW][hapmap];0.80[MEX][hapmap];0.84[YRI][hapmap]
rs4947534	0.83[CHB][hapmap];0.96[YRI][hapmap]
rs4948096	1.00[ASW][hapmap];0.88[YRI][hapmap]
rs4948102	0.90[CHB][hapmap];0.89[JPT][hapmap];0.92[YRI][hapmap]
rs4948104	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4948106	0.81[CHB][hapmap]
rs6593292	0.88[YRI][hapmap]
rs6954546	0.81[AMR][1000 genomes]
rs6958480	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6966609	0.83[AMR][1000 genomes]
rs766333	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7783339	0.85[CHB][hapmap]
rs7793921	0.84[ASW][hapmap];0.92[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs7801169	0.81[CHB][hapmap]
rs7801467	0.84[AMR][1000 genomes]
rs7811270	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs816409	0.81[CHB][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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs6593297	CHCHD2	Cis_1M	lymphoblastoid	RTeQTL
rs6593297	SUMF2	cis	parietal	SCAN
rs6593297	LOC645317	trans	multi-tissue	Pritchard
rs6593297	SUMF2	cis	cerebellum	SCAN
rs6593297	ZNF713	cis	cerebellum	SCAN
rs6593297	GBAS	cis	Thyroid	GTEx
rs6593297	GBAS	cis	parietal	SCAN
rs6593297	FKBP9L	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56120000-56122400	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
2	chr7:56120200-56124000	Weak transcription	Spleen	Spleen
3	chr7:56120200-56125600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr7:56120200-56131200	Weak transcription	Aorta	Aorta
5	chr7:56120400-56122400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr7:56120400-56123000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr7:56120400-56123000	Weak transcription	Ovary	ovary
8	chr7:56120400-56124000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:56120400-56124000	Weak transcription	Gastric	stomach
10	chr7:56120600-56122600	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr7:56120600-56123600	Transcr. at gene 5' and 3'	A549	lung
12	chr7:56120600-56131000	Strong transcription	Adipose Nuclei	Adipose
13	chr7:56120800-56122400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr7:56120800-56122400	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr7:56120800-56122600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr7:56120800-56123000	Weak transcription	Right Ventricle	heart
17	chr7:56120800-56123200	Weak transcription	Psoas Muscle	Psoas
18	chr7:56120800-56123600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr7:56120800-56123800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
20	chr7:56120800-56123800	Weak transcription	Small Intestine	intestine
21	chr7:56120800-56124000	Weak transcription	Esophagus	oesophagus
22	chr7:56120800-56125200	Weak transcription	Colonic Mucosa	Colon
23	chr7:56120800-56127400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr7:56120800-56130000	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr7:56120800-56130400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
26	chr7:56120800-56130800	Strong transcription	Brain Angular Gyrus	brain
27	chr7:56120800-56131200	Strong transcription	Fetal Thymus	thymus
28	chr7:56120800-56131400	Strong transcription	Fetal Muscle Leg	muscle
29	chr7:56120800-56131600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr7:56121000-56122400	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr7:56121000-56122600	Enhancers	Fetal Heart	heart
32	chr7:56121000-56122600	Transcr. at gene 5' and 3'	K562	blood
33	chr7:56121000-56123000	Weak transcription	Primary B cells from cord blood	blood
34	chr7:56121000-56124200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
35	chr7:56121000-56124800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr7:56121000-56130000	Weak transcription	Stomach Mucosa	stomach
37	chr7:56121000-56130800	Strong transcription	Fetal Lung	lung
38	chr7:56121000-56131000	Strong transcription	Brain Anterior Caudate	brain
39	chr7:56121000-56131200	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr7:56121000-56131200	Strong transcription	Brain Hippocampus Middle	brain
41	chr7:56121200-56122200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr7:56121200-56122400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr7:56121200-56123000	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr7:56121200-56123000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr7:56121200-56123000	Weak transcription	Thymus	Thymus
46	chr7:56121200-56123200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr7:56121200-56124000	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr7:56121200-56126000	Strong transcription	Colon Smooth Muscle	Colon
49	chr7:56121200-56128600	Strong transcription	HSMMtube	muscle
50	chr7:56121200-56129400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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