Variant report

Variant	rs58539907
Chromosome Location	chr17:38257940-38257941
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	FOSL1	chr17:38256445-38257974	HCT-116	colon:	n/a	chr17:38257573-38257582 chr17:38257622-38257634 chr17:38257575-38257582 chr17:38257572-38257583
2	HEY1	chr17:38256606-38257951	HepG2	liver:	n/a	n/a
3	HCFC1	chr17:38253428-38258087	Hela-S3	cervix:	n/a	n/a
4	JUND	chr17:38254373-38258017	HCT-116	colon:	n/a	chr17:38257573-38257582 chr17:38255602-38255611 chr17:38255310-38255322 chr17:38255309-38255317 chr17:38257622-38257634 chr17:38255311-38255321 chr17:38257575-38257582 chr17:38255310-38255321 chr17:38255312-38255320 chr17:38257572-38257583 chr17:38255342-38255351
5	POLR2A	chr17:38254246-38257976	Hela-S3	cervix:	n/a	n/a
6	SP1	chr17:38256448-38257945	A549	lung:	n/a	chr17:38257674-38257686 chr17:38257675-38257685 chr17:38257140-38257150 chr17:38257671-38257685 chr17:38257674-38257686 chr17:38257677-38257691 chr17:38257145-38257155 chr17:38256518-38256531 chr17:38257675-38257684
7	TCF7L2	chr17:38256600-38257941	Hela-S3	cervix:	n/a	chr17:38257250-38257260 chr17:38257573-38257582 chr17:38257574-38257583 chr17:38257248-38257262 chr17:38257249-38257263 chr17:38257251-38257260
8	GATA3	chr17:38256329-38257980	A549	lung:	n/a	chr17:38256758-38256767 chr17:38257425-38257435
9	NFIC	chr17:38256598-38258009	HepG2	liver:	n/a	n/a
10	POLR2A	chr17:38253989-38257950	HCT-116	colon:	n/a	n/a
11	SIX5	chr17:38255423-38258048	A549	lung:	n/a	chr17:38257046-38257055 chr17:38257535-38257551 chr17:38257048-38257057
12	MAX	chr17:38256251-38258018	HepG2	liver:	n/a	chr17:38256926-38256935 chr17:38257669-38257679 chr17:38257300-38257309
13	TEAD4	chr17:38256704-38258030	HepG2	liver:	n/a	n/a
14	SP1	chr17:38256164-38258042	HCT-116	colon:	n/a	chr17:38257674-38257686 chr17:38257675-38257685 chr17:38256433-38256447 chr17:38257140-38257150 chr17:38257671-38257685 chr17:38257674-38257686 chr17:38257677-38257691 chr17:38257145-38257155 chr17:38256518-38256531 chr17:38257675-38257684
15	TCF7L2	chr17:38256853-38257960	HepG2	liver:	n/a	chr17:38257250-38257260 chr17:38257573-38257582 chr17:38257574-38257583 chr17:38257248-38257262 chr17:38257249-38257263 chr17:38257251-38257260
16	BCL3	chr17:38254583-38258019	A549	lung:	n/a	chr17:38257671-38257684 chr17:38256678-38256691 chr17:38257574-38257583 chr17:38255605-38255614
17	MAX	chr17:38254425-38257986	A549	lung:	n/a	chr17:38255690-38255700 chr17:38255686-38255701 chr17:38255409-38255418 chr17:38255690-38255699 chr17:38256926-38256935 chr17:38255408-38255419 chr17:38257669-38257679 chr17:38255447-38255457 chr17:38255410-38255417 chr17:38255300-38255310 chr17:38255692-38255701 chr17:38255409-38255419 chr17:38257300-38257309 chr17:38255409-38255418 chr17:38255691-38255698 chr17:38255689-38255700
18	EGR1	chr17:38256381-38257970	HCT-116	colon:	n/a	chr17:38257034-38257058 chr17:38257021-38257030 chr17:38257546-38257560 chr17:38257679-38257689 chr17:38256894-38256903 chr17:38257676-38257689
19	FOSL2	chr17:38256630-38258008	HepG2	liver:	n/a	chr17:38257573-38257582 chr17:38257622-38257634 chr17:38257575-38257582
20	MYBL2	chr17:38256524-38258008	HepG2	liver:	n/a	n/a
21	MAX	chr17:38254087-38258039	HCT-116	colon:	n/a	chr17:38255690-38255700 chr17:38255686-38255701 chr17:38255409-38255418 chr17:38255690-38255699 chr17:38256926-38256935 chr17:38255408-38255419 chr17:38257669-38257679 chr17:38255447-38255457 chr17:38255410-38255417 chr17:38255300-38255310 chr17:38255692-38255701 chr17:38255409-38255419 chr17:38257300-38257309 chr17:38255409-38255418 chr17:38255691-38255698 chr17:38255689-38255700
22	SP1	chr17:38256028-38257960	A549	lung:	n/a	chr17:38257674-38257686 chr17:38257675-38257685 chr17:38256433-38256447 chr17:38257140-38257150 chr17:38257671-38257685 chr17:38257674-38257686 chr17:38257677-38257691 chr17:38257145-38257155 chr17:38256518-38256531 chr17:38257675-38257684
23	TCF12	chr17:38254122-38258026	A549	lung:	n/a	n/a
24	BCL3	chr17:38256359-38257966	A549	lung:	n/a	chr17:38257671-38257684 chr17:38256678-38256691 chr17:38257574-38257583
25	MYC	chr17:38254224-38258534	A549	lung:	n/a	chr17:38255690-38255700 chr17:38255686-38255701 chr17:38255409-38255418 chr17:38255690-38255699 chr17:38256926-38256935 chr17:38255408-38255419 chr17:38257669-38257679 chr17:38255447-38255457 chr17:38255410-38255417 chr17:38255300-38255310 chr17:38255692-38255701 chr17:38255409-38255419 chr17:38257300-38257309 chr17:38255409-38255418 chr17:38255691-38255698 chr17:38255689-38255700
26	MAX	chr17:38254252-38258025	A549	lung:	n/a	chr17:38255690-38255700 chr17:38255686-38255701 chr17:38255409-38255418 chr17:38255690-38255699 chr17:38256926-38256935 chr17:38255408-38255419 chr17:38257669-38257679 chr17:38255447-38255457 chr17:38255410-38255417 chr17:38255300-38255310 chr17:38255692-38255701 chr17:38255409-38255419 chr17:38257300-38257309 chr17:38255409-38255418 chr17:38255691-38255698 chr17:38255689-38255700
27	HEY1	chr17:38254130-38257958	HepG2	liver:	n/a	chr17:38255593-38255608
28	MAZ	chr17:38254070-38258034	IMR90	lung:	n/a	chr17:38255690-38255700 chr17:38255686-38255701 chr17:38255409-38255418 chr17:38255690-38255699 chr17:38256926-38256935 chr17:38255408-38255419 chr17:38257669-38257679 chr17:38255447-38255457 chr17:38255410-38255417 chr17:38255300-38255310 chr17:38255692-38255701 chr17:38255409-38255419 chr17:38257300-38257309 chr17:38255409-38255418 chr17:38255691-38255698 chr17:38255689-38255700
29	EGR1	chr17:38256453-38258040	HCT-116	colon:	n/a	chr17:38257034-38257058 chr17:38257021-38257030 chr17:38257546-38257560 chr17:38257679-38257689 chr17:38256894-38256903 chr17:38257676-38257689
30	POLR2A	chr17:38253857-38257992	HepG2	liver:	n/a	n/a
31	MBD4	chr17:38256642-38258060	HepG2	liver:	n/a	n/a
32	SP1	chr17:38256673-38257994	HepG2	liver:	n/a	chr17:38257674-38257686 chr17:38257675-38257685 chr17:38257140-38257150 chr17:38257671-38257685 chr17:38257674-38257686 chr17:38257677-38257691 chr17:38257145-38257155 chr17:38257675-38257684
33	MBD4	chr17:38256605-38258031	HepG2	liver:	n/a	n/a
34	JUN	chr17:38256617-38258024	K562	blood:	n/a	chr17:38257573-38257582 chr17:38257622-38257634 chr17:38257575-38257582
35	SP1	chr17:38256317-38258030	HCT-116	colon:	n/a	chr17:38257674-38257686 chr17:38257675-38257685 chr17:38256433-38256447 chr17:38257140-38257150 chr17:38257671-38257685 chr17:38257674-38257686 chr17:38257677-38257691 chr17:38257145-38257155 chr17:38256518-38256531 chr17:38257675-38257684

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr17:38257936-38257986	HAEpiC	amniotic membrane:	n/a
2	chr17:38257936-38257986	LNCaP	prostate:	n/a
3	chr17:38257936-38257986	HEEpiC	esophagus:	n/a
4	chr17:38257936-38257986	AG10803	skin:	n/a
5	chr17:38257936-38257986	NHDF-neo	bronchial:	n/a
6	chr17:38257936-38257986	HNPCEpiC	eye:	n/a
7	chr17:38257936-38257986	HIPEpiC	eye:	n/a
8	chr17:38257936-38257986	AG09309	skin:	n/a
9	chr17:38257936-38257986	Jurkat	blood:	n/a
10	chr17:38257936-38257986	ProgFib	skin:	n/a
11	chr17:38257936-38257986	PANC-1	pancreas:	n/a
12	chr17:38257936-38257986	GM12892	blood:	n/a
13	chr17:38257936-38257986	NHBE	bronchial:	n/a
14	chr17:38257936-38257986	SK-N-SH_RA	brain:	n/a
15	chr17:38257936-38257986	HL-60	blood:	n/a
16	chr17:38257936-38257986	RPTEC	kidney:	n/a
17	chr17:38257936-38257986	AG04450	lung:	fetal
18	chr17:38257936-38257986	NT2-D1	testis:	n/a
19	chr17:38257936-38257986	HCPEpiC	choroid plexus:	n/a
20	chr17:38257936-38257986	GM19239	blood:	n/a
21	chr17:38257936-38257986	GM12878	blood:	n/a
22	chr17:38257936-38257986	ovcar-3	ovarian:	n/a
23	chr17:38257936-38257986	T-47D	breast:	n/a
24	chr17:38257936-38257986	AG09319	gingival:	n/a
25	chr17:38257936-38257986	U87	brain:	n/a
26	chr17:38257936-38257986	A549	lung:	n/a
27	chr17:38257936-38257986	BE2_C	brain:	n/a
28	chr17:38257936-38257986	BJ	skin:	n/a
29	chr17:38257936-38257986	HRCEpiC	kidney:	n/a
30	chr17:38257936-38257986	HRPEpiC	eye:	n/a
31	chr17:38257936-38257986	AG04449	skin:	fetal
32	chr17:38257936-38257986	SK-N-SH	brain:	n/a
33	chr17:38257936-38257986	HCF	heart:	n/a
34	chr17:38257936-38257986	K562	blood:	n/a
35	chr17:38257936-38257986	IMR90	lung:	fetal
36	chr17:38257936-38257986	PFSK-1	brain:	n/a
37	chr17:38257936-38257986	HPAEpiC	pulmonary alveolar:	n/a
38	chr17:38257936-38257986	HCT-116	colon:	n/a
39	chr17:38257936-38257986	SK-N-MC	brain:	n/a
40	chr17:38257936-38257986	NH-A	brain:	n/a
41	chr17:38257936-38257986	AoSMC	blood vessel:	n/a
42	chr17:38257936-38257986	GM06990	blood:	n/a
43	chr17:38257936-38257986	SAEC	small airway:	n/a
44	chr17:38257936-38257986	HEK293	kidney:	embryo
45	chr17:38257936-38257986	Caco-2	colon:	n/a
46	chr17:38257936-38257986	HepG2	liver:	n/a
47	chr17:38257936-38257986	HCM	heart:	n/a
48	chr17:38257936-38257986	PrEC	prostate:	n/a
49	chr17:38257936-38257986	SKMC	muscle:	n/a
50	chr17:38257936-38257986	ECC-1	luminal epithelium:	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:38216722..38220271-chr17:38254476..38257952,5	K562	blood:
2	chr17:38252517..38259251-chr17:38276179..38282890,16	MCF-7	breast:
3	chr17:38255433..38258713-chr17:38276171..38280451,4	K562	blood:
4	chr17:38253967..38258330-chr17:38333170..38336526,4	MCF-7	breast:
5	chr17:38257297..38260164-chr17:38470426..38472629,2	MCF-7	breast:
6	chr17:38223608..38228220-chr17:38255265..38258726,4	MCF-7	breast:
7	chr17:38219115..38220777-chr17:38255846..38258790,2	MCF-7	breast:
8	chr17:38255988..38258755-chr17:38294920..38298049,5	MCF-7	breast:
9	chr17:38257287..38258183-chr2:20646387..20646981,2	Hela-S3	cervix:
10	chr17:38224768..38231268-chr17:38252636..38258126,7	K562	blood:

Variant related genes	Relation type
NR1D1	TF binding region
NR1D1	CpG island
ENSG00000108349	Chromatin interaction
ENSG00000008838	Chromatin interaction
ENSG00000126351	Chromatin interaction
ENSG00000143878	Chromatin interaction
ENSG00000108352	Chromatin interaction
ENSG00000188895	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10512481	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57188376	0.86[AFR][1000 genomes]
rs57795122	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59368120	0.86[AFR][1000 genomes]
rs61093245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv908221	chr17:38216522-38289003	Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv833444	chr17:38242823-38437280	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
3	nsv520636	chr17:38254689-38264197	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
4	nsv528369	chr17:38256693-38289003	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38255600-38258000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
2	chr17:38255600-38258000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr17:38256800-38258000	Enhancers	Fetal Heart	heart
4	chr17:38256800-38258200	Enhancers	Lung	lung
5	chr17:38256800-38258800	Enhancers	Spleen	Spleen
6	chr17:38256800-38269800	Weak transcription	Aorta	Aorta
7	chr17:38257000-38258000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr17:38257000-38258000	Flanking Active TSS	Stomach Smooth Muscle	stomach
9	chr17:38257000-38258600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
10	chr17:38257000-38259200	Weak transcription	Gastric	stomach
11	chr17:38257000-38261800	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr17:38257200-38258000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr17:38257200-38258000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr17:38257200-38258000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr17:38257200-38258000	Flanking Active TSS	Liver	Liver
16	chr17:38257200-38258000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
17	chr17:38257200-38258000	Flanking Active TSS	HSMM	muscle
18	chr17:38257200-38258000	Flanking Active TSS	NH-A	brain
19	chr17:38257200-38258000	Flanking Active TSS	Osteobl	bone
20	chr17:38257200-38258200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
21	chr17:38257200-38258400	Flanking Active TSS	Hela-S3	cervix
22	chr17:38257400-38258000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr17:38257400-38258000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr17:38257400-38258000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr17:38257400-38258000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr17:38257400-38258000	Enhancers	Primary B cells from cord blood	blood
27	chr17:38257400-38258000	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr17:38257400-38258000	Enhancers	Fetal Stomach	stomach
29	chr17:38257400-38258000	Flanking Active TSS	A549	lung
30	chr17:38257400-38258400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr17:38257400-38258400	Enhancers	Small Intestine	intestine
32	chr17:38257400-38258400	Flanking Active TSS	HepG2	liver
33	chr17:38257400-38258600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr17:38257400-38258600	Enhancers	Esophagus	oesophagus
35	chr17:38257400-38258600	Enhancers	Fetal Kidney	kidney
36	chr17:38257400-38259000	Weak transcription	Fetal Brain Male	brain
37	chr17:38257400-38259200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr17:38257400-38262000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr17:38257400-38267200	Enhancers	Fetal Muscle Trunk	muscle
40	chr17:38257400-38267200	Enhancers	Fetal Muscle Leg	muscle
41	chr17:38257400-38267400	Enhancers	Fetal Intestine Small	intestine
42	chr17:38257400-38267800	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr17:38257400-38269600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr17:38257400-38269600	Enhancers	Fetal Thymus	thymus
45	chr17:38257600-38258000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr17:38257600-38258000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr17:38257600-38258000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr17:38257600-38258000	Enhancers	Primary neutrophils fromperipheralblood	blood
49	chr17:38257600-38258000	Enhancers	Primary B cells from peripheral blood	blood
50	chr17:38257600-38258000	Enhancers	Primary hematopoietic stem cells short term culture	blood

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