Variant report

Variant	rs2908543
Chromosome Location	chr7:56174924-56174925
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:100)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:100 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr7:56173289-56175642	K562	blood:	n/a	chr7:56173977-56173987 chr7:56173971-56173981
2	MYC	chr7:56174914-56175170	K562	blood:	n/a	n/a
3	MAZ	chr7:56173812-56175768	K562	blood:	n/a	chr7:56173977-56173987 chr7:56173971-56173981
4	CHD1	chr7:56172805-56174968	IMR90	lung:	n/a	n/a
5	GATA2	chr7:56174787-56175300	K562	blood:	n/a	n/a
6	PML	chr7:56174653-56175327	K562	blood:	n/a	n/a
7	ATF1	chr7:56174765-56175305	K562	blood:	n/a	n/a
8	CREB1	chr7:56174612-56175352	K562	blood:	n/a	n/a
9	MXI1	chr7:56173240-56175231	K562	blood:	n/a	chr7:56173817-56173826
10	MAX	chr7:56174830-56175169	K562	blood:	n/a	n/a
11	CBX3	chr7:56174748-56175905	K562	blood:	n/a	n/a
12	MYC	chr7:56173047-56175630	K562	blood:	n/a	chr7:56173977-56173987 chr7:56173971-56173981
13	CEBPD	chr7:56174644-56175309	K562	blood:	n/a	n/a
14	RCOR1	chr7:56174003-56175750	K562	blood:	n/a	n/a
15	EP300	chr7:56173429-56175213	GM12878	blood:	n/a	chr7:56174629-56174639 chr7:56174748-56174762 chr7:56173887-56173900 chr7:56174352-56174359
16	POLR2A	chr7:56172964-56174948	GM12878	blood:	n/a	n/a
17	POLR2A	chr7:56173021-56175328	HepG2	liver:	n/a	n/a
18	IRF1	chr7:56173275-56175820	K562	blood:	n/a	chr7:56174663-56174673 chr7:56174186-56174200 chr7:56174663-56174677
19	CEBPB	chr7:56174696-56175236	K562	blood:	n/a	n/a
20	RFX5	chr7:56173276-56175185	K562	blood:	n/a	n/a
21	POLR2A	chr7:56173624-56175332	K562	blood:	n/a	n/a
22	POLR2A	chr7:56165178-56175093	K562	blood:	n/a	n/a
23	POLR2A	chr7:56174727-56175187	K562	blood:	n/a	n/a
24	POLR2A	chr7:56173115-56175287	K562	blood:	n/a	n/a
25	SPI1	chr7:56174806-56175152	K562	blood:	n/a	n/a
26	GABPA	chr7:56173340-56175094	MCF-7	breast:	n/a	chr7:56173972-56173981
27	GATA2	chr7:56174782-56175259	K562	blood:	n/a	n/a
28	EGR1	chr7:56174737-56175141	K562	blood:	n/a	n/a
29	NR2F2	chr7:56173558-56175358	K562	blood:	n/a	n/a
30	ZMIZ1	chr7:56173157-56175717	K562	blood:	n/a	n/a
31	SPI1	chr7:56174838-56175047	K562	blood:	n/a	n/a
32	CEBPD	chr7:56173891-56175335	K562	blood:	n/a	n/a
33	GATA2	chr7:56174675-56175320	K562	blood:	n/a	n/a
34	GATA1	chr7:56173024-56176382	K562	blood:	n/a	chr7:56174484-56174493
35	TBL1XR1	chr7:56173332-56175468	K562	blood:	n/a	n/a
36	E2F6	chr7:56174866-56175038	K562	blood:	n/a	n/a
37	STAT5A	chr7:56174756-56175197	K562	blood:	n/a	n/a
38	STAT5A	chr7:56174639-56175370	K562	blood:	n/a	n/a
39	CUX1	chr7:56173055-56175194	K562	blood:	n/a	n/a
40	ZNF274	chr7:56174810-56175182	K562	blood:	n/a	n/a
41	E2F4	chr7:56173362-56174941	MCF10A-Er-Src	breast:	n/a	chr7:56174187-56174196 chr7:56173972-56173981
42	POLR2A	chr7:56173041-56174926	MCF10A-Er-Src	breast:	n/a	n/a
43	CCNT2	chr7:56174734-56175501	K562	blood:	n/a	n/a
44	TBP	chr7:56173241-56175285	K562	blood:	n/a	n/a
45	POLR2A	chr7:56173060-56175220	PBDE	blood:	n/a	n/a
46	HEY1	chr7:56174871-56175176	K562	blood:	n/a	n/a
47	TRIM28	chr7:56174837-56175183	K562	blood:	n/a	n/a
48	GATA1	chr7:56173291-56175479	PBDE	blood:	n/a	chr7:56174484-56174493
49	NR2F2	chr7:56174746-56175184	K562	blood:	n/a	n/a
50	BHLHE40	chr7:56173810-56175247	K562	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:56174888-56174938	HRPEpiC	eye:	n/a
2	chr7:56174888-56174938	Jurkat	blood:	n/a
3	chr7:56174888-56174938	NB4	blood:	n/a
4	chr7:56174888-56174938	HMEC	breast:	n/a
5	chr7:56174888-56174938	U87	brain:	n/a
6	chr7:56174888-56174938	SK-N-SH	brain:	n/a
7	chr7:56174888-56174938	AG09309	skin:	n/a
8	chr7:56174888-56174938	HL-60	blood:	n/a
9	chr7:56174888-56174938	HCF	heart:	n/a
10	chr7:56174888-56174938	CMK	blood:	n/a
11	chr7:56174888-56174938	SK-N-MC	brain:	n/a
12	chr7:56174888-56174938	GM12878	blood:	n/a
13	chr7:56174888-56174938	ECC-1	luminal epithelium:	n/a
14	chr7:56174888-56174938	HCM	heart:	n/a
15	chr7:56174888-56174938	HCT-116	colon:	n/a
16	chr7:56174888-56174938	NT2-D1	testis:	n/a
17	chr7:56174888-56174938	SAEC	small airway:	n/a
18	chr7:56174888-56174938	GM12892	blood:	n/a
19	chr7:56174888-56174938	BE2_C	brain:	n/a
20	chr7:56174888-56174938	K562	blood:	n/a
21	chr7:56174888-56174938	H1-hESC	embryonic stem cell:	embryo
22	chr7:56174888-56174938	HIPEpiC	eye:	n/a
23	chr7:56174888-56174938	AoSMC	blood vessel:	n/a
24	chr7:56174888-56174938	T-47D	breast:	n/a
25	chr7:56174888-56174938	NHBE	bronchial:	n/a
26	chr7:56174888-56174938	IMR90	lung:	fetal
27	chr7:56174888-56174938	Hepatocyte	liver:	n/a
28	chr7:56174888-56174938	LNCaP	prostate:	n/a
29	chr7:56174888-56174938	HPAEpiC	pulmonary alveolar:	n/a
30	chr7:56174888-56174938	HUVEC	blood vessel:	n/a
31	chr7:56174888-56174938	AG04450	lung:	fetal
32	chr7:56174888-56174938	MCF10A-Er-Src	breast:	n/a
33	chr7:56174888-56174938	HRCEpiC	kidney:	n/a
34	chr7:56174888-56174938	NHDF-neo	bronchial:	n/a
35	chr7:56174888-56174938	NH-A	brain:	n/a
36	chr7:56174888-56174938	HNPCEpiC	eye:	n/a
37	chr7:56174888-56174938	AG10803	skin:	n/a
38	chr7:56174888-56174938	SK-N-SH_RA	brain:	n/a
39	chr7:56174888-56174938	HRE	kidney:	n/a
40	chr7:56174888-56174938	Caco-2	colon:	n/a
41	chr7:56174888-56174938	HEK293	kidney:	embryo
42	chr7:56174888-56174938	Hela-S3	cervix:	n/a
43	chr7:56174888-56174938	ovcar-3	ovarian:	n/a
44	chr7:56174888-56174938	AG09319	gingival:	n/a
45	chr7:56174888-56174938	HEEpiC	esophagus:	n/a
46	chr7:56174888-56174938	AG04449	skin:	fetal
47	chr7:56174888-56174938	ProgFib	skin:	n/a
48	chr7:56174888-56174938	HepG2	liver:	n/a
49	chr7:56174888-56174938	RPTEC	kidney:	n/a
50	chr7:56174888-56174938	PFSK-1	brain:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:56166954..56169953-chr7:56173700..56175335,2	MCF-7	breast:
2	chr7:56173528..56175860-chr7:56295526..56297795,2	K562	blood:

No data

Variant related genes	Relation type
CHCHD2	TF binding region
CHCHD2	CpG island
ENSG00000238673	Chromatin interaction
ENSG00000227491	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10255049	0.84[ASN][1000 genomes]
rs10258800	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11238394	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11773374	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11773453	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12537943	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13234899	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13242830	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13244654	0.88[CEU][hapmap];0.81[CHB][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1894832	0.85[CEU][hapmap];0.90[AMR][1000 genomes]
rs2002651	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2016482	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2016724	0.88[CEU][hapmap]
rs2242508	0.81[CHB][hapmap]
rs2331180	0.84[CEU][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2538047	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2908544	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2908545	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2908550	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4947536	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4948106	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6593297	0.81[CHB][hapmap]
rs6945795	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7782243	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7783339	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7793921	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7799471	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7801169	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs816408	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs816409	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs816411	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs860118	0.85[CEU][hapmap]
rs933466	0.84[CEU][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9767946	0.82[AMR][1000 genomes];0.86[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

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56172200-56175000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr7:56172600-56175000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr7:56172600-56175000	Active TSS	HSMM	muscle
4	chr7:56172800-56175000	Active TSS	NHLF	lung
5	chr7:56173000-56175000	Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr7:56173000-56175000	Active TSS	Right Atrium	heart
7	chr7:56173000-56175200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
8	chr7:56173200-56175000	Active TSS	NH-A	brain
9	chr7:56173200-56175000	Active TSS	NHEK	skin
10	chr7:56173400-56175000	Active TSS	Adipose Nuclei	Adipose
11	chr7:56173400-56175000	Active TSS	Brain Anterior Caudate	brain
12	chr7:56173400-56175000	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr7:56173400-56175000	Active TSS	Fetal Thymus	thymus
14	chr7:56173400-56175000	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr7:56173400-56175000	Active TSS	HSMMtube	muscle
16	chr7:56173400-56175000	Active TSS	Osteobl	bone
17	chr7:56173400-56175200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr7:56173400-56175200	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr7:56173400-56175200	Active TSS	K562	blood
20	chr7:56173600-56175000	Active TSS	Duodenum Mucosa	Duodenum
21	chr7:56173600-56175200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr7:56173600-56175200	Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr7:56173600-56175200	Active TSS	Stomach Smooth Muscle	stomach
24	chr7:56174200-56175000	Flanking Active TSS	Primary hematopoietic stem cells	blood
25	chr7:56174200-56183600	Weak transcription	Gastric	stomach
26	chr7:56174400-56175000	Flanking Active TSS	Primary B cells from cord blood	blood
27	chr7:56174400-56175000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
28	chr7:56174400-56175000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr7:56174400-56175200	Flanking Active TSS	Dnd41	blood
30	chr7:56174400-56175400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
31	chr7:56174400-56176200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr7:56174600-56175000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
33	chr7:56174600-56175000	Flanking Active TSS	Primary B cells from peripheral blood	blood
34	chr7:56174600-56175000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
35	chr7:56174600-56175000	Flanking Active TSS	Fetal Kidney	kidney
36	chr7:56174600-56175000	Enhancers	Stomach Mucosa	stomach
37	chr7:56174600-56175200	Flanking Active TSS	Primary T cells from cord blood	blood
38	chr7:56174600-56175200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
39	chr7:56174600-56175400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
40	chr7:56174600-56175400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
41	chr7:56174600-56175600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
42	chr7:56174600-56175600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr7:56174800-56175000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr7:56174800-56175000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr7:56174800-56175000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr7:56174800-56175000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr7:56174800-56175000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr7:56174800-56175000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
49	chr7:56174800-56175000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
50	chr7:56174800-56175000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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