Variant report

Variant	rs7548467
Chromosome Location	chr1:78444734-78444735
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:439)
CpG islands
(count:61)
Chromatin interactive
region (count:24)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:439 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F6	chr1:78443937-78445363	K562	blood:	n/a	n/a
2	STAT5A	chr1:78443720-78444793	GM12878	blood:	n/a	chr1:78443827-78443836 chr1:78443826-78443835
3	MYBL2	chr1:78444512-78445440	HepG2	liver:	n/a	n/a
4	TBP	chr1:78443742-78445474	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr1:78443593-78446070	GM12892	blood:	n/a	n/a
6	POLR2A	chr1:78443736-78445403	GM12891	blood:	n/a	n/a
7	POLR2A	chr1:78442194-78445438	GM12878	blood:	n/a	n/a
8	WRNIP1	chr1:78443823-78445370	GM12878	blood:	n/a	n/a
9	E2F6	chr1:78444695-78444955	K562	blood:	n/a	n/a
10	E2F6	chr1:78444696-78445275	A549	lung:	n/a	n/a
11	BCL3	chr1:78444705-78445283	A549	lung:	n/a	n/a
12	POLR2A	chr1:78444559-78445284	HepG2	liver:	n/a	n/a
13	TAL1	chr1:78443548-78445565	K562	blood:	n/a	n/a
14	SP4	chr1:78444552-78445335	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr1:78443756-78445435	GM12891	blood:	n/a	n/a
16	MYC	chr1:78443937-78445363	K562	blood:	n/a	n/a
17	ATF1	chr1:78444445-78445383	K562	blood:	n/a	n/a
18	POLR2A	chr1:78443969-78445417	HCT-116	colon:	n/a	n/a
19	YY1	chr1:78444381-78445269	K562	blood:	n/a	n/a
20	ZBTB33	chr1:78444461-78445383	HepG2	liver:	n/a	chr1:78444834-78444849
21	POLR2A	chr1:78444319-78445378	A549	lung:	n/a	n/a
22	TAF1	chr1:78443810-78445348	H1-neurons	neurons:	n/a	n/a
23	MYC	chr1:78443790-78445449	K562	blood:	n/a	n/a
24	REST	chr1:78444567-78444809	A549	lung:	n/a	n/a
25	EP300	chr1:78443547-78445474	GM12878	blood:	n/a	n/a
26	CEBPD	chr1:78444598-78445272	HepG2	liver:	n/a	n/a
27	BRCA1	chr1:78444453-78445394	H1-hESC	embryonic stem cell:	n/a	chr1:78444836-78444845
28	TCF12	chr1:78443737-78445422	A549	lung:	n/a	n/a
29	RELA	chr1:78443774-78445415	GM12891	blood:	n/a	n/a
30	MAX	chr1:78443814-78445460	K562	blood:	n/a	n/a
31	ZBTB33	chr1:78443804-78445430	HCT-116	colon:	n/a	chr1:78444834-78444849
32	RAD21	chr1:78444717-78445578	Hela-S3	cervix:	n/a	n/a
33	TBL1XR1	chr1:78444252-78445293	K562	blood:	n/a	n/a
34	POLR2A	chr1:78444303-78445374	MCF-7	breast:	n/a	n/a
35	MAX	chr1:78444234-78445437	H1-hESC	embryonic stem cell:	n/a	n/a
36	MAX	chr1:78444631-78445400	MCF-7	breast:	n/a	n/a
37	POLR2A	chr1:78443568-78445574	PBDE	blood:	n/a	n/a
38	MAX	chr1:78443762-78445538	ECC-1	luminal epithelium:	n/a	n/a
39	RELA	chr1:78443809-78445565	GM19099	blood:	n/a	n/a
40	GTF2F1	chr1:78444373-78445337	K562	blood:	n/a	n/a
41	KAT2A	chr1:78444591-78445152	GM12878	blood:	n/a	n/a
42	CHD2	chr1:78443759-78445477	GM12878	blood:	n/a	chr1:78444836-78444845
43	POLR2A	chr1:78443696-78445441	H1-neurons	neurons:	n/a	n/a
44	MYC	chr1:78444409-78445375	MCF-7	breast:	n/a	n/a
45	POLR2A	chr1:78443332-78446830	MCF10A-Er-Src	breast:	n/a	n/a
46	TAF7	chr1:78443760-78445474	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr1:78443783-78445418	HepG2	liver:	n/a	n/a
48	YY1	chr1:78443818-78445351	K562	blood:	n/a	chr1:78443981-78443997 chr1:78443985-78443993
49	TBL1XR1	chr1:78443467-78445330	K562	blood:	n/a	n/a
50	CREB1	chr1:78443808-78445462	GM12878	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:78444712-78444762	HUVEC	blood vessel:	n/a
2	chr1:78444712-78444762	RPTEC	kidney:	n/a
3	chr1:78444712-78444762	HepG2	liver:	n/a
4	chr1:78444712-78444762	SK-N-SH	brain:	n/a
5	chr1:78444712-78444762	Hepatocyte	liver:	n/a
6	chr1:78444712-78444762	HEEpiC	esophagus:	n/a
7	chr1:78444712-78444762	HNPCEpiC	eye:	n/a
8	chr1:78444712-78444762	A549	lung:	n/a
9	chr1:78444712-78444762	GM12891	blood:	n/a
10	chr1:78444712-78444762	H1-hESC	embryonic stem cell:	embryo
11	chr1:78444712-78444762	AG10803	skin:	n/a
12	chr1:78444712-78444762	Caco-2	colon:	n/a
13	chr1:78444712-78444762	HRPEpiC	eye:	n/a
14	chr1:78444712-78444762	HEK293	kidney:	embryo
15	chr1:78444712-78444762	SAEC	small airway:	n/a
16	chr1:78444712-78444762	SKMC	muscle:	n/a
17	chr1:78444712-78444762	NT2-D1	testis:	n/a
18	chr1:78444712-78444762	GM12878	blood:	n/a
19	chr1:78444712-78444762	HL-60	blood:	n/a
20	chr1:78444712-78444762	AoSMC	blood vessel:	n/a
21	chr1:78444712-78444762	LNCaP	prostate:	n/a
22	chr1:78444712-78444762	IMR90	lung:	fetal
23	chr1:78444712-78444762	ProgFib	skin:	n/a
24	chr1:78444712-78444762	T-47D	breast:	n/a
25	chr1:78444712-78444762	SK-N-MC	brain:	n/a
26	chr1:78444712-78444762	HIPEpiC	eye:	n/a
27	chr1:78444712-78444762	PrEC	prostate:	n/a
28	chr1:78444712-78444762	HRE	kidney:	n/a
29	chr1:78444712-78444762	HRCEpiC	kidney:	n/a
30	chr1:78444712-78444762	AG09319	gingival:	n/a
31	chr1:78444712-78444762	BJ	skin:	n/a
32	chr1:78444712-78444762	BE2_C	brain:	n/a
33	chr1:78444712-78444762	SK-N-SH_RA	brain:	n/a
34	chr1:78444712-78444762	AG09309	skin:	n/a
35	chr1:78444712-78444762	CMK	blood:	n/a
36	chr1:78444712-78444762	ECC-1	luminal epithelium:	n/a
37	chr1:78444712-78444762	GM19239	blood:	n/a
38	chr1:78444712-78444762	MCF-7	breast:	n/a
39	chr1:78444712-78444762	HCPEpiC	choroid plexus:	n/a
40	chr1:78444712-78444762	NHDF-neo	bronchial:	n/a
41	chr1:78444712-78444762	PANC-1	pancreas:	n/a
42	chr1:78444712-78444762	GM06990	blood:	n/a
43	chr1:78444712-78444762	ovcar-3	ovarian:	n/a
44	chr1:78444712-78444762	HMEC	breast:	n/a
45	chr1:78444712-78444762	Hela-S3	cervix:	n/a
46	chr1:78444712-78444762	NH-A	brain:	n/a
47	chr1:78444712-78444762	MCF10A-Er-Src	breast:	n/a
48	chr1:78444712-78444762	K562	blood:	n/a
49	chr1:78444712-78444762	AG04449	skin:	fetal
50	chr1:78444712-78444762	HPAEpiC	pulmonary alveolar:	n/a

(count:24 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:78444381..78445068-chr10:89577628..89578293,2	HCT-116	colon:
2	chr1:27648655..27649314-chr1:78444243..78445194,2	HCT-116	colon:
3	chr1:78419725..78422750-chr1:78442650..78445885,3	MCF-7	breast:
4	chr1:78411683..78415390-chr1:78442833..78445980,4	MCF-7	breast:
5	chr1:78444303..78445105-chr8:95835200..95836118,2	Hela-S3	cervix:
6	chr1:78444372..78445367-chr17:48943462..48944118,2	NB4	blood:
7	chr1:78444592..78445398-chr16:18812644..18813329,2	Hela-S3	cervix:
8	chr1:78444323..78445294-chr3:150125728..150126525,2	Hela-S3	cervix:
9	chr1:78444284..78444857-chr12:6602401..6603010,2	Hela-S3	cervix:
10	chr1:78193577..78195378-chr1:78443583..78446391,2	K562	blood:
11	chr1:78444410..78445296-chr1:156470434..156471041,2	NB4	blood:
12	chr1:78443931..78444821-chr20:39969045..39969848,2	Hela-S3	cervix:
13	chr1:78441900..78447727-chr1:78466477..78473207,15	MCF-7	breast:
14	chr1:78165656..78168470-chr1:78443418..78445028,2	K562	blood:
15	chr1:78147609..78151437-chr1:78443386..78446443,6	K562	blood:
16	chr1:78444284..78445055-chr7:73497660..73498624,2	Hela-S3	cervix:
17	chr1:78223072..78225558-chr1:78443212..78444913,3	K562	blood:
18	chr1:78444226..78444832-chr20:37554586..37555473,2	NB4	blood:
19	chr1:78146715..78149884-chr1:78444203..78446027,3	MCF-7	breast:
20	chr1:78441980..78446801-chr1:78467462..78471771,12	MCF-7	breast:
21	chr1:78444687..78445239-chr6:30687625..30688493,2	Hela-S3	cervix:
22	chr1:78444248..78445167-chr6:27860541..27861272,2	Hela-S3	cervix:
23	chr1:78444510..78445277-chr22:43411075..43411781,2	Hela-S3	cervix:
24	chr1:78444432..78445064-chr15:72524130..72524851,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
DNAJB4	TF binding region
GIPC2	TF binding region
DNAJB4	CpG island
GIPC2	CpG island
ENSG00000138138	Chromatin interaction
ENSG00000196428	Chromatin interaction
ENSG00000260342	Chromatin interaction
ENSG00000273338	Chromatin interaction
ENSG00000116604	Chromatin interaction
ENSG00000223820	Chromatin interaction
ENSG00000067225	Chromatin interaction
ENSG00000196230	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000036549	Chromatin interaction
ENSG00000229980	Chromatin interaction
ENSG00000010292	Chromatin interaction
ENSG00000141232	Chromatin interaction
ENSG00000132793	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000100266	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000162616	Chromatin interaction
ENSG00000162613	Chromatin interaction
ENSG00000164941	Chromatin interaction
ENSG00000077254	Chromatin interaction
ENSG00000111639	Chromatin interaction
ENSG00000170540	Chromatin interaction
ENSG00000186501	Chromatin interaction
ENSG00000106683	Chromatin interaction
ENSG00000101447	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs41312643	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6604877	1.00[CEU][hapmap]
rs6666107	0.83[EUR][1000 genomes]
rs6679645	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs6686829	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6694656	1.00[YRI][hapmap]
rs74092331	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7523258	1.00[CEU][hapmap]
rs7549028	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9659817	1.00[CEU][hapmap]
rs9661421	1.00[CEU][hapmap];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1794082	chr1:78102426-78492221	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	esv3434340	chr1:78153780-78607103	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv518855	chr1:78416669-78456355	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78440200-78445200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
2	chr1:78441200-78446200	Active TSS	Aorta	Aorta
3	chr1:78441400-78446800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr1:78441600-78446000	Active TSS	Colonic Mucosa	Colon
5	chr1:78441800-78445600	Active TSS	Skeletal Muscle Male	skeletal muscle
6	chr1:78441800-78446200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:78442000-78446200	Active TSS	Brain Angular Gyrus	brain
8	chr1:78442000-78446800	Active TSS	GM12878-XiMat	blood
9	chr1:78442000-78447200	Active TSS	A549	lung
10	chr1:78442200-78445800	Active TSS	Duodenum Mucosa	Duodenum
11	chr1:78442200-78446600	Active TSS	H9 Cell Line	embryonic stem cell
12	chr1:78442400-78446000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:78442400-78446200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:78442600-78445600	Active TSS	Stomach Smooth Muscle	stomach
15	chr1:78442600-78446000	Active TSS	Esophagus	oesophagus
16	chr1:78442600-78446000	Active TSS	Gastric	stomach
17	chr1:78442600-78446000	Active TSS	Ovary	ovary
18	chr1:78442600-78446200	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr1:78442600-78446200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:78442600-78446200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr1:78442600-78446200	Active TSS	Psoas Muscle	Psoas
22	chr1:78442600-78446400	Active TSS	H1 Cell Line	embryonic stem cell
23	chr1:78442600-78446600	Active TSS	Right Atrium	heart
24	chr1:78442600-78447000	Active TSS	Right Ventricle	heart
25	chr1:78442800-78445800	Active TSS	Brain Cingulate Gyrus	brain
26	chr1:78442800-78445800	Active TSS	Fetal Heart	heart
27	chr1:78442800-78446000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:78442800-78446000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:78442800-78446000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr1:78442800-78446000	Active TSS	Brain Anterior Caudate	brain
31	chr1:78442800-78446000	Active TSS	Pancreas	Pancrea
32	chr1:78442800-78446200	Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr1:78442800-78446200	Active TSS	Brain Inferior Temporal Lobe	brain
34	chr1:78442800-78446200	Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr1:78442800-78446200	Active TSS	Fetal Intestine Large	intestine
36	chr1:78442800-78446200	Active TSS	Hela-S3	cervix
37	chr1:78442800-78446400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr1:78442800-78446400	Active TSS	K562	blood
39	chr1:78442800-78446400	Active TSS	NHDF-Ad	bronchial
40	chr1:78442800-78446600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
41	chr1:78442800-78446600	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr1:78442800-78446600	Active TSS	Fetal Kidney	kidney
43	chr1:78442800-78446600	Active TSS	NHLF	lung
44	chr1:78442800-78446800	Active TSS	ES-I3 Cell Line	embryonic stem cell
45	chr1:78442800-78447200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:78442800-78447200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr1:78443000-78445800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
48	chr1:78443000-78445800	Active TSS	Fetal Lung	lung
49	chr1:78443000-78445800	Active TSS	Rectal Mucosa Donor 31	rectum
50	chr1:78443000-78445800	Active TSS	Osteobl	bone

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