Variant report

Variant	rs7563499
Chromosome Location	chr2:172290497-172290498
allele	A/G
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	POLR2A	chr2:172289567-172291438	NB4	blood:	n/a	n/a
2	REST	chr2:172290077-172291609	H1-neurons	neurons:	n/a	chr2:172290567-172290577
3	IRF1	chr2:172289738-172291403	K562	blood:	n/a	chr2:172290257-172290271 chr2:172290655-172290669
4	RCOR1	chr2:172290086-172291380	GM12878	blood:	n/a	n/a
5	CREB1	chr2:172290170-172291434	H1-hESC	embryonic stem cell:	n/a	n/a
6	GABPA	chr2:172290315-172291360	A549	lung:	n/a	chr2:172290572-172290581 chr2:172291072-172291081 chr2:172290939-172290948
7	ZBTB7A	chr2:172290240-172290749	K562	blood:	n/a	chr2:172290573-172290582
8	YY1	chr2:172290348-172291231	SK-N-SH	brain:	n/a	chr2:172291014-172291025 chr2:172291007-172291021 chr2:172290704-172290713 chr2:172290637-172290651 chr2:172291008-172291022
9	POLR2A	chr2:172290240-172291462	MCF-7	breast:	n/a	n/a
10	YY1	chr2:172289837-172291400	HepG2	liver:	n/a	chr2:172291014-172291025 chr2:172291007-172291021 chr2:172290704-172290713 chr2:172290637-172290651 chr2:172291008-172291022
11	TAF1	chr2:172290131-172291464	H1-hESC	embryonic stem cell:	n/a	n/a
12	ZNF143	chr2:172289787-172291311	GM12878	blood:	n/a	n/a
13	POLR2A	chr2:172289575-172291439	GM18526	blood:	n/a	n/a
14	MYC	chr2:172289572-172291366	HepG2	liver:	n/a	n/a
15	CHD2	chr2:172289723-172291368	K562	blood:	n/a	n/a
16	FOXP2	chr2:172290299-172290804	SK-N-MC	brain:	n/a	n/a
17	MAZ	chr2:172289834-172291379	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr2:172289645-172291536	HUVEC	blood vessel:	n/a	n/a
19	POLR2A	chr2:172290318-172291380	HUVEC	blood vessel:	n/a	n/a
20	SIX5	chr2:172290480-172290975	K562	blood:	n/a	n/a
21	CTCF	chr2:172290420-172290570	MCF-7	breast:	n/a	n/a
22	HEY1	chr2:172289502-172291483	HepG2	liver:	n/a	chr2:172291071-172291086 chr2:172290660-172290675 chr2:172291011-172291026 chr2:172290569-172290584
23	CTCF	chr2:172290195-172291094	H1-hESC	embryonic stem cell:	n/a	n/a
24	EP300	chr2:172290454-172290526	K562	blood:	n/a	n/a
25	NR3C1	chr2:172290186-172290760	A549	lung:	n/a	n/a
26	ETS1	chr2:172290309-172291382	K562	blood:	n/a	chr2:172290704-172290715
27	MAZ	chr2:172289558-172291438	GM12878	blood:	n/a	n/a
28	PML	chr2:172289483-172291649	GM12878	blood:	n/a	n/a
29	POLR2A	chr2:172289530-172291475	GM18951	blood:	n/a	n/a
30	REST	chr2:172289512-172291445	HL-60	blood:	n/a	chr2:172290567-172290577
31	POLR2A	chr2:172288779-172291571	GM12891	blood:	n/a	n/a
32	ELF1	chr2:172290246-172291284	A549	lung:	n/a	n/a
33	USF1	chr2:172290426-172290866	SK-N-SH_RA	brain:	n/a	chr2:172290790-172290806
34	POLR2A	chr2:172289497-172291505	HL-60	blood:	n/a	n/a
35	BATF	chr2:172290283-172290586	GM12878	blood:	n/a	n/a
36	CTCF	chr2:172290460-172290610	AG04450	lung:	n/a	n/a
37	POLR2A	chr2:172289495-172291445	K562	blood:	n/a	n/a
38	CREB1	chr2:172290251-172291377	A549	lung:	n/a	n/a
39	POLR2A	chr2:172289523-172291431	HL-60	blood:	n/a	n/a
40	CTCF	chr2:172290480-172290630	AoAF	blood vessel:	n/a	n/a
41	SP1	chr2:172290122-172290868	H1-hESC	embryonic stem cell:	n/a	chr2:172290511-172290522 chr2:172290655-172290667 chr2:172290656-172290665 chr2:172290657-172290666 chr2:172290652-172290666 chr2:172290655-172290667
42	TAF1	chr2:172290168-172291359	Hela-S3	cervix:	n/a	n/a
43	JUND	chr2:172289217-172291375	K562	blood:	n/a	chr2:172290944-172290953
44	POLR2A	chr2:172289533-172291582	K562	blood:	n/a	n/a
45	POLR2A	chr2:172289586-172291446	GM19099	blood:	n/a	n/a
46	EBF1	chr2:172290257-172290843	GM12878	blood:	n/a	n/a
47	SP1	chr2:172290165-172290880	HepG2	liver:	n/a	chr2:172290511-172290522 chr2:172290655-172290667 chr2:172290656-172290665 chr2:172290657-172290666 chr2:172290652-172290666 chr2:172290655-172290667
48	SIN3AK20	chr2:172290135-172291480	K562	blood:	n/a	n/a
49	HA-E2F1	chr2:172290365-172291423	Hela-S3	cervix:	n/a	chr2:172290656-172290665 chr2:172291011-172291021 chr2:172290704-172290713 chr2:172291078-172291087 chr2:172290572-172290581
50	FOXA1	chr2:172290104-172291354	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:172289860..172292485-chr2:175259037..175261189,2	MCF-7	breast:
2	chr2:171810262..171812279-chr2:172288795..172291435,2	K562	blood:
3	chr12:6862329..6862861-chr2:172289776..172290506,2	Hela-S3	cervix:
4	chr2:171784160..171787954-chr2:172288133..172292253,10	K562	blood:
5	chr12:120729306..120729877-chr2:172290109..172290816,2	Hela-S3	cervix:
6	chr1:6673077..6674019-chr2:172290205..172290705,2	NB4	blood:
7	chr2:172289123..172292836-chr2:172306272..172310763,6	K562	blood:
8	chr2:172288399..172297381-chr2:172370978..172381493,22	K562	blood:
9	chr2:172015340..172019166-chr2:172288878..172291883,5	K562	blood:
10	chr2:171785354..171787093-chr2:172289682..172291292,2	MCF-7	breast:
11	chr19:12902292..12903141-chr2:172289942..172290847,2	Hela-S3	cervix:
12	chr2:172288832..172292910-chr2:172322388..172326341,4	K562	blood:
13	chr1:117908627..117911250-chr2:172289062..172291364,2	MCF-7	breast:
14	chr2:172289876..172292562-chr2:172333814..172336703,3	K562	blood:
15	chr2:172014091..172018646-chr2:172288530..172293107,15	MCF-7	breast:
16	chr2:172013226..172020125-chr2:172287594..172292844,18	MCF-7	breast:
17	chr2:172289978..172291717-chr2:172966936..172969521,2	K562	blood:
18	chr2:172287317..172289847-chr2:172289909..172292066,2	MCF-7	breast:
19	chr2:172013756..172019540-chr2:172285624..172293532,16	K562	blood:
20	chr17:27919198..27919858-chr2:172289871..172290707,2	Hela-S3	cervix:
21	chr2:171784119..171787322-chr2:172288781..172292051,4	MCF-7	breast:
22	chr2:172287467..172293160-chr2:172293206..172300397,21	K562	blood:
23	chr2:171783791..171787349-chr2:172286549..172291928,9	K562	blood:
24	chr2:172288399..172293582-chr2:172376630..172381034,10	K562	blood:
25	chr2:172289880..172292267-chr2:172966936..172969958,3	K562	blood:
26	chr2:172287753..172291848-chr2:172543733..172546489,4	K562	blood:
27	chr2:172289011..172290991-chr2:172749560..172752051,2	K562	blood:

Variant related genes	Relation type
METTL8	TF binding region
DCAF17	TF binding region
ENSG00000115827	Chromatin interaction
ENSG00000236651	Chromatin interaction
ENSG00000198586	Chromatin interaction
ENSG00000115844	Chromatin interaction
ENSG00000123600	Chromatin interaction
ENSG00000115840	Chromatin interaction
ENSG00000089693	Chromatin interaction
ENSG00000198162	Chromatin interaction
ENSG00000171223	Chromatin interaction
ENSG00000144306	Chromatin interaction
ENSG00000233762	Chromatin interaction
ENSG00000264647	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000116273	Chromatin interaction
ENSG00000071967	Chromatin interaction
ENSG00000077380	Chromatin interaction
ENSG00000138433	Chromatin interaction
ENSG00000115806	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs16859392	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16859394	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57396064	0.98[AFR][1000 genomes]
rs57999878	0.80[AFR][1000 genomes]
rs58033547	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs58560571	0.82[AFR][1000 genomes]
rs58796565	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59745257	1.00[AFR][1000 genomes]
rs59886446	0.90[AFR][1000 genomes]
rs60100357	1.00[AFR][1000 genomes]
rs60837517	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs61731491	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs62183501	0.80[AFR][1000 genomes]
rs66525413	0.90[AFR][1000 genomes]
rs73021082	0.90[AFR][1000 genomes]
rs73022904	1.00[AFR][1000 genomes]
rs73022907	1.00[AFR][1000 genomes]
rs73022921	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs73022930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73022949	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7564602	0.82[AFR][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	esv3382346	chr2:172062677-172363892	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	esv3349868	chr2:172276494-172302401	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
3	esv1832950	chr2:172283513-172488111	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 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	chr2:172289000-172292400	Active TSS	GM12878-XiMat	blood
2	chr2:172289200-172291800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:172289200-172292000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:172289200-172292000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:172289200-172292000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:172289200-172292400	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr2:172289400-172291600	Active TSS	Fetal Kidney	kidney
8	chr2:172289400-172291800	Active TSS	Colonic Mucosa	Colon
9	chr2:172289400-172292400	Active TSS	Fetal Brain Female	brain
10	chr2:172289400-172292400	Active TSS	A549	lung
11	chr2:172289600-172290600	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr2:172289600-172291800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr2:172289800-172291200	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr2:172289800-172291400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:172289800-172291400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
16	chr2:172289800-172291400	Active TSS	Esophagus	oesophagus
17	chr2:172289800-172291600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr2:172289800-172291600	Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr2:172289800-172291600	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr2:172289800-172291800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr2:172289800-172291800	Active TSS	H9 Cell Line	embryonic stem cell
22	chr2:172289800-172291800	Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr2:172289800-172291800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr2:172289800-172291800	Active TSS	Psoas Muscle	Psoas
25	chr2:172289800-172291800	Active TSS	Hela-S3	cervix
26	chr2:172289800-172292000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr2:172289800-172292000	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr2:172289800-172292000	Active TSS	NHEK	skin
29	chr2:172289800-172292000	Active TSS	NHLF	lung
30	chr2:172289800-172292200	Active TSS	H1 Cell Line	embryonic stem cell
31	chr2:172289800-172292200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr2:172289800-172292400	Active TSS	HMEC	breast
33	chr2:172290000-172290800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr2:172290000-172291000	Active TSS	Stomach Mucosa	stomach
35	chr2:172290000-172291200	Transcr. at gene 5' and 3'	Right Atrium	heart
36	chr2:172290000-172291200	Active TSS	HSMMtube	muscle
37	chr2:172290000-172291200	Active TSS	NH-A	brain
38	chr2:172290000-172291400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr2:172290000-172291400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:172290000-172291400	Active TSS	Primary T helper cells PMA-I stimulated	--
41	chr2:172290000-172291400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr2:172290000-172291400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
43	chr2:172290000-172291400	Active TSS	Gastric	stomach
44	chr2:172290000-172291400	Active TSS	Lung	lung
45	chr2:172290000-172291400	Active TSS	Sigmoid Colon	Sigmoid Colon
46	chr2:172290000-172291400	Active TSS	Small Intestine	intestine
47	chr2:172290000-172291600	Active TSS	HUES64 Cell Line	embryonic stem cell
48	chr2:172290000-172291600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr2:172290000-172291600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr2:172290000-172291600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin

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