Variant report

Variant	rs62085937
Chromosome Location	chr17:66453941-66453942
allele	A/C
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	JUND	chr17:66453448-66454718	K562	blood:	n/a	n/a
2	MBD4	chr17:66453822-66454750	HepG2	liver:	n/a	n/a
3	JUN	chr17:66453523-66455078	K562	blood:	n/a	n/a
4	POLR2A	chr17:66453924-66454333	K562	blood:	n/a	n/a
5	ELF1	chr17:66453723-66454330	GM12878	blood:	n/a	n/a
6	HDAC2	chr17:66453715-66454484	MCF-7	breast:	n/a	n/a
7	SP2	chr17:66453667-66454213	HepG2	liver:	n/a	chr17:66453892-66453907 chr17:66453919-66453934 chr17:66453864-66453879
8	NFYB	chr17:66453478-66454292	GM12878	blood:	n/a	chr17:66453873-66453888
9	CREB1	chr17:66453201-66454778	GM12878	blood:	n/a	n/a
10	USF1	chr17:66453569-66454216	SK-N-SH_RA	brain:	n/a	n/a
11	POLR2A	chr17:66453711-66454313	H1-neurons	neurons:	n/a	n/a
12	GABPA	chr17:66453681-66454186	K562	blood:	n/a	n/a
13	POLR2A	chr17:66453885-66454295	U87	brain:	n/a	n/a
14	USF1	chr17:66453633-66454346	HCT-116	colon:	n/a	n/a
15	RFX5	chr17:66453751-66454194	GM12878	blood:	n/a	n/a
16	RUNX3	chr17:66453777-66454329	GM12878	blood:	n/a	n/a
17	JUND	chr17:66453736-66454168	HepG2	liver:	n/a	n/a
18	BRCA1	chr17:66453803-66454145	Hela-S3	cervix:	n/a	n/a
19	ATF1	chr17:66453764-66454408	K562	blood:	n/a	n/a
20	EGR1	chr17:66453724-66454122	H1-hESC	embryonic stem cell:	n/a	n/a
21	CEBPB	chr17:66453802-66454072	HepG2	liver:	n/a	n/a
22	ATF2	chr17:66453817-66454807	GM12878	blood:	n/a	n/a
23	ZKSCAN1	chr17:66453795-66454321	Hela-S3	cervix:	n/a	n/a
24	NRF1	chr17:66453882-66454576	GM12878	blood:	n/a	n/a
25	POLR2A	chr17:66453825-66454363	HCT-116	colon:	n/a	n/a
26	TBP	chr17:66453892-66454194	H1-hESC	embryonic stem cell:	n/a	n/a
27	MAX	chr17:66453702-66454276	K562	blood:	n/a	chr17:66453986-66453995 chr17:66453986-66453995 chr17:66453985-66453996 chr17:66453986-66453995 chr17:66453985-66453995 chr17:66453984-66453999 chr17:66453984-66453993 chr17:66453815-66453825
28	E2F6	chr17:66453776-66454307	A549	lung:	n/a	chr17:66453959-66453966
29	USF2	chr17:66453407-66454584	GM12878	blood:	n/a	chr17:66453984-66453995
30	SP1	chr17:66452330-66454533	HCT-116	colon:	n/a	chr17:66453896-66453907 chr17:66453446-66453460 chr17:66454133-66454142 chr17:66453920-66453929 chr17:66453864-66453875 chr17:66453939-66453960 chr17:66453864-66453876 chr17:66454132-66454141 chr17:66453807-66453816 chr17:66453864-66453876 chr17:66454132-66454141 chr17:66453286-66453296 chr17:66453805-66453817
31	USF1	chr17:66453712-66454102	H1-hESC	embryonic stem cell:	n/a	n/a
32	NFYA	chr17:66453671-66454276	Hela-S3	cervix:	n/a	n/a
33	USF2	chr17:66453756-66454170	HepG2	liver:	n/a	chr17:66453984-66453995
34	USF1	chr17:66453720-66454103	HepG2	liver:	n/a	n/a
35	GTF2F1	chr17:66453912-66454231	Hela-S3	cervix:	n/a	n/a
36	SP1	chr17:66453549-66454181	K562	blood:	n/a	chr17:66453896-66453907 chr17:66454133-66454142 chr17:66453920-66453929 chr17:66453864-66453875 chr17:66453939-66453960 chr17:66453864-66453876 chr17:66454132-66454141 chr17:66453807-66453816 chr17:66453864-66453876 chr17:66454132-66454141 chr17:66453805-66453817
37	POLR2A	chr17:66453900-66454779	GM12891	blood:	n/a	n/a
38	USF1	chr17:66453697-66454128	A549	lung:	n/a	n/a
39	SP2	chr17:66453711-66454083	K562	blood:	n/a	chr17:66453892-66453907 chr17:66453919-66453934 chr17:66453864-66453879
40	SREBP2	chr17:66453736-66454114	HepG2	liver:	n/a	n/a
41	CTCF	chr17:66453823-66453987	GM12878	blood:	n/a	n/a
42	MAX	chr17:66453506-66454475	MCF-7	breast:	n/a	chr17:66453986-66453995 chr17:66453986-66453995 chr17:66453985-66453996 chr17:66453986-66453995 chr17:66453985-66453995 chr17:66453984-66453999 chr17:66453984-66453993 chr17:66453815-66453825
43	CREB1	chr17:66453711-66454078	A549	lung:	n/a	n/a
44	HEY1	chr17:66453919-66454245	HepG2	liver:	n/a	n/a
45	POLR2A	chr17:66453358-66454386	GM10847	blood:	n/a	n/a
46	GATA3	chr17:66453874-66454276	T-47D	breast:	n/a	n/a
47	MAX	chr17:66453368-66454398	NB4	blood:	n/a	chr17:66453986-66453995 chr17:66453986-66453995 chr17:66453985-66453996 chr17:66453986-66453995 chr17:66453985-66453995 chr17:66453984-66453999 chr17:66453984-66453993 chr17:66453815-66453825
48	MAX	chr17:66452311-66454385	HepG2	liver:	n/a	chr17:66453986-66453995 chr17:66453986-66453995 chr17:66453985-66453996 chr17:66453986-66453995 chr17:66453985-66453995 chr17:66453984-66453999 chr17:66453984-66453993 chr17:66453815-66453825
49	CEBPB	chr17:66453763-66454140	IMR90	lung:	n/a	n/a
50	SIN3AK20	chr17:66453716-66454473	HepG2	liver:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr17:66453912-66453962	HNPCEpiC	eye:	n/a
2	chr17:66453912-66453962	RPTEC	kidney:	n/a
3	chr17:66453919-66453969	NHDF-neo	bronchial:	n/a
4	chr17:66453919-66453969	HCM	heart:	n/a
5	chr17:66453912-66453962	AG04450	lung:	fetal
6	chr17:66453919-66453969	PANC-1	pancreas:	n/a
7	chr17:66453912-66453962	SK-N-MC	brain:	n/a
8	chr17:66453912-66453962	HL-60	blood:	n/a
9	chr17:66453919-66453969	HUVEC	blood vessel:	n/a
10	chr17:66453919-66453969	U87	brain:	n/a
11	chr17:66453919-66453969	NT2-D1	testis:	n/a
12	chr17:66453919-66453969	RPTEC	kidney:	n/a
13	chr17:66453919-66453969	ECC-1	luminal epithelium:	n/a
14	chr17:66453912-66453962	HCM	heart:	n/a
15	chr17:66453912-66453962	AG09309	skin:	n/a
16	chr17:66453919-66453969	CMK	blood:	n/a
17	chr17:66453912-66453962	HIPEpiC	eye:	n/a
18	chr17:66453919-66453969	T-47D	breast:	n/a
19	chr17:66453912-66453962	AoSMC	blood vessel:	n/a
20	chr17:66453912-66453962	PFSK-1	brain:	n/a
21	chr17:66453912-66453962	HRCEpiC	kidney:	n/a
22	chr17:66453919-66453969	MCF-7	breast:	n/a
23	chr17:66453919-66453969	HCPEpiC	choroid plexus:	n/a
24	chr17:66453919-66453969	NB4	blood:	n/a
25	chr17:66453919-66453969	H1-hESC	embryonic stem cell:	embryo
26	chr17:66453919-66453969	HMEC	breast:	n/a
27	chr17:66453919-66453969	GM12878	blood:	n/a
28	chr17:66453912-66453962	ovcar-3	ovarian:	n/a
29	chr17:66453912-66453962	GM19239	blood:	n/a
30	chr17:66453919-66453969	IMR90	lung:	fetal
31	chr17:66453912-66453962	HepG2	liver:	n/a
32	chr17:66453919-66453969	HCF	heart:	n/a
33	chr17:66453919-66453969	HAEpiC	amniotic membrane:	n/a
34	chr17:66453912-66453962	H1-hESC	embryonic stem cell:	embryo
35	chr17:66453919-66453969	SK-N-SH	brain:	n/a
36	chr17:66453912-66453962	Hela-S3	cervix:	n/a
37	chr17:66453912-66453962	IMR90	lung:	fetal
38	chr17:66453919-66453969	Caco-2	colon:	n/a
39	chr17:66453912-66453962	A549	lung:	n/a
40	chr17:66453912-66453962	GM12878	blood:	n/a
41	chr17:66453919-66453969	Jurkat	blood:	n/a
42	chr17:66453912-66453962	HEK293	kidney:	embryo
43	chr17:66453919-66453969	PrEC	prostate:	n/a
44	chr17:66453919-66453969	SKMC	muscle:	n/a
45	chr17:66453919-66453969	AG09319	gingival:	n/a
46	chr17:66453912-66453962	PANC-1	pancreas:	n/a
47	chr17:66453912-66453962	ECC-1	luminal epithelium:	n/a
48	chr17:66453912-66453962	AG09319	gingival:	n/a
49	chr17:66453919-66453969	NHBE	bronchial:	n/a
50	chr17:66453912-66453962	PrEC	prostate:	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:66030966..66032993-chr17:66452479..66455259,2	K562	blood:
2	chr17:66030471..66033206-chr17:66450900..66454415,3	MCF-7	breast:
3	chr17:66251565..66253379-chr17:66453840..66455605,2	K562	blood:
4	chr17:66286038..66290193-chr17:66450658..66456945,10	MCF-7	breast:
5	chr17:66242276..66246117-chr17:66451301..66455927,10	MCF-7	breast:
6	chr17:66286653..66288832-chr17:66452442..66454123,2	K562	blood:
7	chr17:66451996..66456192-chr17:66506725..66511948,5	MCF-7	breast:
8	chr17:66394957..66397009-chr17:66453203..66454984,2	K562	blood:
9	chr17:66286653..66290195-chr17:66452394..66455654,6	K562	blood:
10	chr11:61099775..61100323-chr17:66453381..66454210,2	Hela-S3	cervix:
11	chr17:66244200..66246851-chr17:66452530..66455268,2	K562	blood:
12	chr17:66452513..66457853-chr17:66506674..66510981,7	MCF-7	breast:
13	chr17:65988743..65991174-chr17:66452610..66455269,2	MCF-7	breast:
14	chr17:66241762..66247031-chr17:66451924..66454846,13	MCF-7	breast:
15	chr17:66341305..66343019-chr17:66452901..66454766,2	MCF-7	breast:

Variant related genes	Relation type
WIPI1	TF binding region
WIPI1	CpG island
ENSG00000182481	Chromatin interaction
ENSG00000108932	Chromatin interaction
ENSG00000186665	Chromatin interaction
ENSG00000196704	Chromatin interaction
ENSG00000265100	Chromatin interaction
ENSG00000167986	Chromatin interaction
ENSG00000108946	Chromatin interaction
ENSG00000141337	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs2302784	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3785612	0.88[ASN][1000 genomes]
rs55785206	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56233149	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7209319	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833523	chr17:66343323-66510461	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	31 gene(s)	inside rSNPs	diseases
2	esv3344280	chr17:66452382-66455230	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 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	chr17:66450800-66454400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr17:66450800-66454800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr17:66451400-66454400	Active TSS	NHLF	lung
4	chr17:66451600-66454800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr17:66451600-66454800	Active TSS	Right Atrium	heart
6	chr17:66451800-66454000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr17:66451800-66454400	Active TSS	NHDF-Ad	bronchial
8	chr17:66452000-66454200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr17:66452000-66454400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr17:66452000-66454400	Active TSS	Brain Angular Gyrus	brain
11	chr17:66452000-66454600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr17:66452000-66454600	Active TSS	Aorta	Aorta
13	chr17:66452000-66454800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr17:66452000-66454800	Active TSS	Right Ventricle	heart
15	chr17:66452200-66454600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr17:66452200-66454600	Active TSS	Ovary	ovary
17	chr17:66452400-66454400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr17:66452400-66454400	Active TSS	H9 Cell Line	embryonic stem cell
19	chr17:66452400-66454400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr17:66452400-66454400	Active TSS	Lung	lung
21	chr17:66452400-66454600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr17:66452600-66454200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr17:66452600-66454200	Active TSS	Small Intestine	intestine
24	chr17:66452600-66454400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr17:66452600-66454400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr17:66452600-66454400	Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr17:66452600-66454400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr17:66452600-66454400	Active TSS	Brain Inferior Temporal Lobe	brain
29	chr17:66452600-66454400	Active TSS	Esophagus	oesophagus
30	chr17:66452600-66454400	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr17:66452600-66454400	Active TSS	Gastric	stomach
32	chr17:66452600-66454600	Active TSS	H1 Cell Line	embryonic stem cell
33	chr17:66452600-66454600	Active TSS	Colonic Mucosa	Colon
34	chr17:66452800-66454000	Active TSS	Cortex derived primary cultured neurospheres	brain
35	chr17:66452800-66454200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr17:66452800-66454200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr17:66452800-66454200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr17:66452800-66454200	Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr17:66452800-66454200	Active TSS	Muscle Satellite Cultured Cells	--
40	chr17:66452800-66454200	Active TSS	Fetal Lung	lung
41	chr17:66452800-66454200	Active TSS	Hela-S3	cervix
42	chr17:66452800-66454200	Active TSS	HSMMtube	muscle
43	chr17:66452800-66454400	Active TSS	ES-I3 Cell Line	embryonic stem cell
44	chr17:66452800-66454400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr17:66452800-66454400	Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr17:66452800-66454400	Active TSS	iPS-15b Cell Line	embryonic stem cell
47	chr17:66452800-66454400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr17:66452800-66454400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr17:66452800-66454400	Active TSS	Brain Cingulate Gyrus	brain
50	chr17:66452800-66454400	Active TSS	Colon Smooth Muscle	Colon

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