Variant report

Variant	rs17101109
Chromosome Location	chr1:78445468-78445469
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:115)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:115 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TBP	chr1:78443742-78445474	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr1:78443593-78446070	GM12892	blood:	n/a	n/a
3	TAL1	chr1:78443548-78445565	K562	blood:	n/a	n/a
4	EP300	chr1:78443547-78445474	GM12878	blood:	n/a	n/a
5	RAD21	chr1:78444717-78445578	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr1:78443568-78445574	PBDE	blood:	n/a	n/a
7	MAX	chr1:78443762-78445538	ECC-1	luminal epithelium:	n/a	n/a
8	RELA	chr1:78443809-78445565	GM19099	blood:	n/a	n/a
9	CHD2	chr1:78443759-78445477	GM12878	blood:	n/a	chr1:78444836-78444845
10	POLR2A	chr1:78443332-78446830	MCF10A-Er-Src	breast:	n/a	n/a
11	TAF7	chr1:78443760-78445474	H1-hESC	embryonic stem cell:	n/a	n/a
12	PAX5	chr1:78445450-78445835	GM12878	blood:	n/a	n/a
13	CHD1	chr1:78443223-78445655	H1-hESC	embryonic stem cell:	n/a	chr1:78444836-78444845
14	ZBTB33	chr1:78444435-78445522	SK-N-SH	brain:	n/a	chr1:78444834-78444849
15	KAP1	chr1:78443144-78445743	HEK293	kidney:	n/a	n/a
16	RCOR1	chr1:78443787-78445536	GM12878	blood:	n/a	n/a
17	TBP	chr1:78443754-78446127	K562	blood:	n/a	n/a
18	POLR2A	chr1:78443223-78445898	IMR90	lung:	n/a	n/a
19	PML	chr1:78443767-78445524	K562	blood:	n/a	n/a
20	POLR2A	chr1:78443707-78445874	GM12892	blood:	n/a	n/a
21	ATF2	chr1:78444532-78445515	H1-hESC	embryonic stem cell:	n/a	n/a
22	PML	chr1:78443525-78445472	K562	blood:	n/a	n/a
23	MYBL2	chr1:78444496-78445483	HepG2	liver:	n/a	n/a
24	POLR2A	chr1:78443610-78445477	PANC-1	pancreas:	n/a	n/a
25	MAX	chr1:78443689-78445540	HepG2	liver:	n/a	n/a
26	MXI1	chr1:78443882-78445506	K562	blood:	n/a	n/a
27	POLR2A	chr1:78443836-78445897	Raji	blood:	n/a	n/a
28	SIN3AK20	chr1:78443594-78445613	MCF-7	breast:	n/a	n/a
29	MAX	chr1:78443723-78446030	NB4	blood:	n/a	n/a
30	POLR2A	chr1:78443528-78445551	Hela-S3	cervix:	n/a	n/a
31	ZBTB33	chr1:78443805-78445514	A549	lung:	n/a	chr1:78444834-78444849
32	CREB1	chr1:78444463-78445507	H1-hESC	embryonic stem cell:	n/a	n/a
33	SMARCB1	chr1:78443923-78445927	Hela-S3	cervix:	n/a	n/a
34	ATF2	chr1:78443553-78445512	GM12878	blood:	n/a	n/a
35	POLR2A	chr1:78443744-78445476	HEK293	kidney:	n/a	n/a
36	MXI1	chr1:78443808-78445471	HepG2	liver:	n/a	n/a
37	MAX	chr1:78443713-78445478	SK-N-SH	brain:	n/a	n/a
38	POLR2A	chr1:78443129-78445525	GM12892	blood:	n/a	n/a
39	BHLHE40	chr1:78443529-78445989	GM12878	blood:	n/a	n/a
40	POLR2A	chr1:78443523-78445507	MCF10A-Er-Src	breast:	n/a	n/a
41	POLR2A	chr1:78443578-78445488	HUVEC	blood vessel:	n/a	n/a
42	CREB1	chr1:78443672-78445541	K562	blood:	n/a	n/a
43	SIN3A	chr1:78443356-78445567	H1-hESC	embryonic stem cell:	n/a	n/a
44	IRF1	chr1:78443514-78445587	K562	blood:	n/a	chr1:78444810-78444824 chr1:78443953-78443964
45	TAF1	chr1:78443672-78445480	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr1:78443634-78445543	GM12891	blood:	n/a	n/a
47	SIN3AK20	chr1:78444391-78445473	HCT-116	colon:	n/a	n/a
48	STAT3	chr1:78444936-78445578	GM12878	blood:	n/a	n/a
49	MAX	chr1:78443861-78445478	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr1:78443506-78446030	Hela-S3	cervix:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:78444790..78445968-chr1:78469428..78470562,4	Hela-S3	cervix:
2	chr1:78419725..78422750-chr1:78442650..78445885,3	MCF-7	breast:
3	chr1:78411683..78415390-chr1:78442833..78445980,4	MCF-7	breast:
4	chr1:78193577..78195378-chr1:78443583..78446391,2	K562	blood:
5	chr1:78441900..78447727-chr1:78466477..78473207,15	MCF-7	breast:
6	chr1:78147609..78151437-chr1:78443386..78446443,6	K562	blood:
7	chr1:78146715..78149884-chr1:78444203..78446027,3	MCF-7	breast:
8	chr1:78441980..78446801-chr1:78467462..78471771,12	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DNAJB4-1	chr1:78444779-78456066	NONHSAT004062

No data

Variant related genes	Relation type
DNAJB4	TF binding region
FUBP1	TF binding region
ENSG00000036549	Chromatin interaction
ENSG00000273338	Chromatin interaction
ENSG00000077254	Chromatin interaction
ENSG00000162616	Chromatin interaction
ENSG00000162613	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1135921	1.00[AMR][1000 genomes]
rs17100941	1.00[AMR][1000 genomes]
rs17101048	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17101052	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17101082	1.00[CHB][hapmap];0.96[ASN][1000 genomes]
rs2228247	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2296455	1.00[CHB][hapmap];0.96[ASN][1000 genomes]
rs28362659	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28362660	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34128192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3767026	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3767027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56325960	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59087988	0.95[ASN][1000 genomes]
rs72685391	0.96[ASN][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	chr1:78441200-78446200	Active TSS	Aorta	Aorta
2	chr1:78441400-78446800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr1:78441600-78446000	Active TSS	Colonic Mucosa	Colon
4	chr1:78441800-78445600	Active TSS	Skeletal Muscle Male	skeletal muscle
5	chr1:78441800-78446200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:78442000-78446200	Active TSS	Brain Angular Gyrus	brain
7	chr1:78442000-78446800	Active TSS	GM12878-XiMat	blood
8	chr1:78442000-78447200	Active TSS	A549	lung
9	chr1:78442200-78445800	Active TSS	Duodenum Mucosa	Duodenum
10	chr1:78442200-78446600	Active TSS	H9 Cell Line	embryonic stem cell
11	chr1:78442400-78446000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:78442400-78446200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:78442600-78445600	Active TSS	Stomach Smooth Muscle	stomach
14	chr1:78442600-78446000	Active TSS	Esophagus	oesophagus
15	chr1:78442600-78446000	Active TSS	Gastric	stomach
16	chr1:78442600-78446000	Active TSS	Ovary	ovary
17	chr1:78442600-78446200	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr1:78442600-78446200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:78442600-78446200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr1:78442600-78446200	Active TSS	Psoas Muscle	Psoas
21	chr1:78442600-78446400	Active TSS	H1 Cell Line	embryonic stem cell
22	chr1:78442600-78446600	Active TSS	Right Atrium	heart
23	chr1:78442600-78447000	Active TSS	Right Ventricle	heart
24	chr1:78442800-78445800	Active TSS	Brain Cingulate Gyrus	brain
25	chr1:78442800-78445800	Active TSS	Fetal Heart	heart
26	chr1:78442800-78446000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr1:78442800-78446000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:78442800-78446000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr1:78442800-78446000	Active TSS	Brain Anterior Caudate	brain
30	chr1:78442800-78446000	Active TSS	Pancreas	Pancrea
31	chr1:78442800-78446200	Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr1:78442800-78446200	Active TSS	Brain Inferior Temporal Lobe	brain
33	chr1:78442800-78446200	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr1:78442800-78446200	Active TSS	Fetal Intestine Large	intestine
35	chr1:78442800-78446200	Active TSS	Hela-S3	cervix
36	chr1:78442800-78446400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:78442800-78446400	Active TSS	K562	blood
38	chr1:78442800-78446400	Active TSS	NHDF-Ad	bronchial
39	chr1:78442800-78446600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr1:78442800-78446600	Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr1:78442800-78446600	Active TSS	Fetal Kidney	kidney
42	chr1:78442800-78446600	Active TSS	NHLF	lung
43	chr1:78442800-78446800	Active TSS	ES-I3 Cell Line	embryonic stem cell
44	chr1:78442800-78447200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr1:78442800-78447200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr1:78443000-78445800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
47	chr1:78443000-78445800	Active TSS	Fetal Lung	lung
48	chr1:78443000-78445800	Active TSS	Rectal Mucosa Donor 31	rectum
49	chr1:78443000-78445800	Active TSS	Osteobl	bone
50	chr1:78443000-78446000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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