Variant report

Variant	rs2952293
Chromosome Location	chr17:66454017-66454018
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	TAF1	chr17:66453970-66454131	GM12892	blood:	n/a	n/a
10	CREB1	chr17:66453201-66454778	GM12878	blood:	n/a	n/a
11	USF1	chr17:66453569-66454216	SK-N-SH_RA	brain:	n/a	n/a
12	POLR2A	chr17:66453711-66454313	H1-neurons	neurons:	n/a	n/a
13	GABPA	chr17:66453681-66454186	K562	blood:	n/a	n/a
14	POLR2A	chr17:66453885-66454295	U87	brain:	n/a	n/a
15	USF1	chr17:66453633-66454346	HCT-116	colon:	n/a	n/a
16	RFX5	chr17:66453751-66454194	GM12878	blood:	n/a	n/a
17	RUNX3	chr17:66453777-66454329	GM12878	blood:	n/a	n/a
18	JUND	chr17:66453736-66454168	HepG2	liver:	n/a	n/a
19	BRCA1	chr17:66453803-66454145	Hela-S3	cervix:	n/a	n/a
20	ATF1	chr17:66453764-66454408	K562	blood:	n/a	n/a
21	EGR1	chr17:66453724-66454122	H1-hESC	embryonic stem cell:	n/a	n/a
22	CEBPB	chr17:66453802-66454072	HepG2	liver:	n/a	n/a
23	ATF2	chr17:66453817-66454807	GM12878	blood:	n/a	n/a
24	ZKSCAN1	chr17:66453795-66454321	Hela-S3	cervix:	n/a	n/a
25	NRF1	chr17:66453882-66454576	GM12878	blood:	n/a	n/a
26	POLR2A	chr17:66453825-66454363	HCT-116	colon:	n/a	n/a
27	TBP	chr17:66453892-66454194	H1-hESC	embryonic stem cell:	n/a	n/a
28	MYC	chr17:66453994-66454019	HepG2	liver:	n/a	n/a
29	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
30	E2F6	chr17:66453776-66454307	A549	lung:	n/a	chr17:66453959-66453966
31	USF2	chr17:66453407-66454584	GM12878	blood:	n/a	chr17:66453984-66453995
32	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
33	USF1	chr17:66453712-66454102	H1-hESC	embryonic stem cell:	n/a	n/a
34	NFYA	chr17:66453671-66454276	Hela-S3	cervix:	n/a	n/a
35	USF2	chr17:66453756-66454170	HepG2	liver:	n/a	chr17:66453984-66453995
36	USF1	chr17:66453720-66454103	HepG2	liver:	n/a	n/a
37	GTF2F1	chr17:66453912-66454231	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr17:66453960-66454245	H1-hESC	embryonic stem cell:	n/a	n/a
39	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
40	CTCF	chr17:66454000-66454150	AG04449	skin:	n/a	n/a
41	POLR2A	chr17:66453900-66454779	GM12891	blood:	n/a	n/a
42	USF1	chr17:66453697-66454128	A549	lung:	n/a	n/a
43	SP2	chr17:66453711-66454083	K562	blood:	n/a	chr17:66453892-66453907 chr17:66453919-66453934 chr17:66453864-66453879
44	SREBP2	chr17:66453736-66454114	HepG2	liver:	n/a	n/a
45	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
46	CREB1	chr17:66453711-66454078	A549	lung:	n/a	n/a
47	POLR2A	chr17:66453946-66454189	H1-hESC	embryonic stem cell:	n/a	n/a
48	HEY1	chr17:66453919-66454245	HepG2	liver:	n/a	n/a
49	POLR2A	chr17:66453358-66454386	GM10847	blood:	n/a	n/a
50	GATA3	chr17:66453874-66454276	T-47D	breast:	n/a	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
ENSG00000182481	Chromatin interaction
ENSG00000141337	Chromatin interaction
ENSG00000186665	Chromatin interaction
ENSG00000196704	Chromatin interaction
ENSG00000108946	Chromatin interaction
ENSG00000167986	Chromatin interaction
ENSG00000108932	Chromatin interaction
ENSG00000265100	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10153240	0.82[EUR][1000 genomes]
rs1108683	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2909208	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2909210	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67556103	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs883622	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs888298	0.94[EUR][1000 genomes];0.93[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	chr17:66451800-66454400	Active TSS	NHDF-Ad	bronchial
7	chr17:66452000-66454200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr17:66452000-66454400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr17:66452000-66454400	Active TSS	Brain Angular Gyrus	brain
10	chr17:66452000-66454600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr17:66452000-66454600	Active TSS	Aorta	Aorta
12	chr17:66452000-66454800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr17:66452000-66454800	Active TSS	Right Ventricle	heart
14	chr17:66452200-66454600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr17:66452200-66454600	Active TSS	Ovary	ovary
16	chr17:66452400-66454400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr17:66452400-66454400	Active TSS	H9 Cell Line	embryonic stem cell
18	chr17:66452400-66454400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr17:66452400-66454400	Active TSS	Lung	lung
20	chr17:66452400-66454600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr17:66452600-66454200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr17:66452600-66454200	Active TSS	Small Intestine	intestine
23	chr17:66452600-66454400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr17:66452600-66454400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr17:66452600-66454400	Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr17:66452600-66454400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr17:66452600-66454400	Active TSS	Brain Inferior Temporal Lobe	brain
28	chr17:66452600-66454400	Active TSS	Esophagus	oesophagus
29	chr17:66452600-66454400	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr17:66452600-66454400	Active TSS	Gastric	stomach
31	chr17:66452600-66454600	Active TSS	H1 Cell Line	embryonic stem cell
32	chr17:66452600-66454600	Active TSS	Colonic Mucosa	Colon
33	chr17:66452800-66454200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr17:66452800-66454200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr17:66452800-66454200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr17:66452800-66454200	Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr17:66452800-66454200	Active TSS	Muscle Satellite Cultured Cells	--
38	chr17:66452800-66454200	Active TSS	Fetal Lung	lung
39	chr17:66452800-66454200	Active TSS	Hela-S3	cervix
40	chr17:66452800-66454200	Active TSS	HSMMtube	muscle
41	chr17:66452800-66454400	Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr17:66452800-66454400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr17:66452800-66454400	Active TSS	HUES64 Cell Line	embryonic stem cell
44	chr17:66452800-66454400	Active TSS	iPS-15b Cell Line	embryonic stem cell
45	chr17:66452800-66454400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr17:66452800-66454400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr17:66452800-66454400	Active TSS	Brain Cingulate Gyrus	brain
48	chr17:66452800-66454400	Active TSS	Colon Smooth Muscle	Colon
49	chr17:66452800-66454400	Active TSS	Fetal Kidney	kidney
50	chr17:66452800-66454400	Active TSS	A549	lung

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