Variant report

Variant	rs17797090
Chromosome Location	chr12:104324266-104324267
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	GABPA	chr12:104322837-104324464	SK-N-SH	brain:	n/a	chr12:104323616-104323625 chr12:104324137-104324146
2	ZNF143	chr12:104322493-104324458	GM12878	blood:	n/a	chr12:104324141-104324159 chr12:104323579-104323597 chr12:104323586-104323595 chr12:104323536-104323554 chr12:104324136-104324146 chr12:104323540-104323559 chr12:104324429-104324447
3	RCOR1	chr12:104323737-104325674	GM12878	blood:	n/a	n/a
4	EBF1	chr12:104322093-104325000	GM12878	blood:	n/a	n/a
5	ETS1	chr12:104324040-104324436	K562	blood:	n/a	chr12:104324054-104324067 chr12:104324145-104324156 chr12:104324052-104324067 chr12:104324137-104324148
6	IRF1	chr12:104323129-104324338	K562	blood:	n/a	chr12:104324147-104324156 chr12:104323289-104323303
7	RUNX3	chr12:104321971-104325533	GM12878	blood:	n/a	n/a
8	BCL3	chr12:104322865-104324368	A549	lung:	n/a	chr12:104323616-104323629 chr12:104323586-104323594 chr12:104323615-104323624 chr12:104323613-104323626
9	CHD2	chr12:104323166-104325167	Hela-S3	cervix:	n/a	chr12:104324650-104324660
10	UBTF	chr12:104323788-104324971	K562	blood:	n/a	n/a
11	E2F6	chr12:104324047-104324303	K562	blood:	n/a	chr12:104324137-104324146
12	TAF1	chr12:104324013-104324504	K562	blood:	n/a	n/a
13	CCNT2	chr12:104323855-104324629	K562	blood:	n/a	chr12:104324230-104324239
14	TAF1	chr12:104324080-104324453	GM12891	blood:	n/a	n/a
15	FOXM1	chr12:104323642-104324502	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr12:104322428-104325591	SK-N-MC	brain:	n/a	n/a
17	WRNIP1	chr12:104322092-104325599	GM12878	blood:	n/a	n/a
18	NFIC	chr12:104322006-104324995	GM12878	blood:	n/a	n/a
19	JUND	chr12:104322907-104324569	A549	lung:	n/a	chr12:104324044-104324053 chr12:104323621-104323630 chr12:104323993-104324002 chr12:104323613-104323622 chr12:104324060-104324069 chr12:104323617-104323626 chr12:104323618-104323627
20	YY1	chr12:104322867-104324436	GM12892	blood:	n/a	chr12:104323616-104323625 chr12:104323613-104323622 chr12:104323287-104323301 chr12:104323621-104323630 chr12:104323613-104323624 chr12:104323626-104323634
21	POLR2A	chr12:104322498-104325320	GM12878	blood:	n/a	n/a
22	REST	chr12:104324029-104324358	Hela-S3	cervix:	n/a	chr12:104324037-104324046
23	MYC	chr12:104322591-104324497	K562	blood:	n/a	chr12:104324136-104324146 chr12:104324419-104324429 chr12:104323780-104323789 chr12:104323784-104323793 chr12:104323936-104323951 chr12:104324369-104324379
24	MAX	chr12:104322072-104325169	GM12878	blood:	n/a	chr12:104324136-104324146 chr12:104322562-104322569 chr12:104324993-104325000 chr12:104324419-104324429 chr12:104323780-104323789 chr12:104324642-104324652 chr12:104323784-104323793 chr12:104323936-104323951 chr12:104322561-104322572 chr12:104324369-104324379
25	PML	chr12:104323943-104324659	K562	blood:	n/a	n/a
26	ELF1	chr12:104323053-104324268	A549	lung:	n/a	chr12:104323827-104323838 chr12:104323825-104323838 chr12:104323287-104323296
27	MXI1	chr12:104323090-104325397	Hela-S3	cervix:	n/a	chr12:104323780-104323795 chr12:104323778-104323793
28	YY1	chr12:104323792-104324440	K562	blood:	n/a	n/a
29	CREB1	chr12:104323728-104324276	A549	lung:	n/a	n/a
30	YY1	chr12:104323258-104324887	ECC-1	luminal epithelium:	n/a	chr12:104323616-104323625 chr12:104323613-104323622 chr12:104323287-104323301 chr12:104323621-104323630 chr12:104323613-104323624 chr12:104323626-104323634
31	MYC	chr12:104323016-104325167	K562	blood:	n/a	chr12:104324136-104324146 chr12:104324993-104325000 chr12:104324419-104324429 chr12:104323780-104323789 chr12:104324642-104324652 chr12:104323784-104323793 chr12:104323936-104323951 chr12:104324369-104324379
32	ETS1	chr12:104323211-104324491	K562	blood:	n/a	chr12:104323829-104323846 chr12:104324054-104324067 chr12:104323829-104323838 chr12:104323829-104323838 chr12:104324145-104324156 chr12:104323616-104323627 chr12:104323830-104323840 chr12:104324052-104324067 chr12:104323829-104323846 chr12:104323585-104323598 chr12:104324137-104324148 chr12:104323586-104323599 chr12:104323829-104323838
33	SIN3AK20	chr12:104324033-104324474	PFSK-1	brain:	n/a	n/a
34	GABPA	chr12:104323008-104324431	SK-N-SH	brain:	n/a	chr12:104323616-104323625 chr12:104324137-104324146
35	NFYA	chr12:104323414-104324487	Hela-S3	cervix:	n/a	chr12:104323989-104324004 chr12:104324043-104324057 chr12:104323989-104324007 chr12:104323988-104324000 chr12:104324042-104324057 chr12:104323989-104324003 chr12:104324038-104324056 chr12:104323991-104324001 chr12:104324079-104324089 chr12:104323989-104324004 chr12:104324042-104324057
36	RELA	chr12:104321990-104325291	GM19193	blood:	n/a	n/a
37	NFYB	chr12:104323499-104324500	K562	blood:	n/a	chr12:104323989-104324004 chr12:104324043-104324057 chr12:104323986-104324001 chr12:104323988-104324000 chr12:104324042-104324057 chr12:104323989-104324003 chr12:104323991-104324001 chr12:104324079-104324089 chr12:104323989-104324004 chr12:104324042-104324057
38	SPI1	chr12:104323885-104324354	GM12878	blood:	n/a	n/a
39	SIX5	chr12:104322968-104324401	A549	lung:	n/a	chr12:104323586-104323595 chr12:104323588-104323597 chr12:104323585-104323599
40	USF1	chr12:104323676-104324416	H1-hESC	embryonic stem cell:	n/a	n/a
41	MYC	chr12:104323722-104324548	H1-hESC	embryonic stem cell:	n/a	chr12:104324136-104324146 chr12:104324419-104324429 chr12:104323780-104323789 chr12:104323784-104323793 chr12:104323936-104323951 chr12:104324369-104324379
42	GTF2F1	chr12:104324031-104324445	K562	blood:	n/a	n/a
43	EGR1	chr12:104323347-104324643	MCF-7	breast:	n/a	chr12:104323616-104323626 chr12:104323615-104323625 chr12:104324238-104324251 chr12:104323535-104323559 chr12:104324059-104324072 chr12:104324058-104324073 chr12:104323616-104323631 chr12:104324059-104324072 chr12:104323617-104323630 chr12:104323574-104323598 chr12:104323620-104323630 chr12:104324239-104324253 chr12:104323617-104323630
44	CREB1	chr12:104322959-104324558	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr12:104324019-104325080	HEK293	kidney:	n/a	n/a
46	TBL1XR1	chr12:104323393-104324445	K562	blood:	n/a	n/a
47	CBX3	chr12:104323280-104324548	K562	blood:	n/a	n/a
48	ZNF143	chr12:104323002-104324370	K562	blood:	n/a	chr12:104324141-104324159 chr12:104323579-104323597 chr12:104323586-104323595 chr12:104323536-104323554 chr12:104324136-104324146 chr12:104323540-104323559
49	TCF12	chr12:104324010-104324380	GM12878	blood:	n/a	chr12:104324029-104324036
50	HMGN3	chr12:104323794-104324467	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:104298858..104303101-chr12:104321689..104325332,4	K562	blood:
2	chr12:104323793..104324401-chr17:2240030..2240794,2	HCT-116	colon:
3	chr11:45826321..45826854-chr12:104324067..104324712,2	Hela-S3	cervix:
4	chr12:104320418..104331406-chr12:104346801..104355501,25	MCF-7	breast:
5	chr12:104233909..104239694-chr12:104322835..104327398,8	K562	blood:
6	chr12:104324118..104324690-chr4:128981820..128982436,2	Hela-S3	cervix:
7	chr12:104233715..104236918-chr12:104321893..104325386,6	K562	blood:
8	chr12:104319631..104321504-chr12:104324248..104326474,2	MCF-7	breast:
9	chr12:104319225..104328292-chr12:104356282..104362179,14	K562	blood:
10	chr12:104322684..104325586-chr12:104530441..104532019,2	K562	blood:
11	chr12:104276117..104279238-chr12:104322705..104326968,4	K562	blood:
12	chr12:104323749..104324657-chr16:22447825..22448729,2	NB4	blood:
13	chr12:104322943..104325215-chr12:104358408..104360868,4	MCF-7	breast:
14	chr12:104324174..104324837-chr17:41322968..41323623,2	Hela-S3	cervix:
15	chr1:46152208..46153875-chr12:104323647..104326577,2	K562	blood:
16	chr12:104323735..104324496-chr17:41465696..41466303,2	NB4	blood:
17	chr12:104323659..104328405-chr12:104357607..104360751,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000214198	TF binding region
ENSG00000111696	Chromatin interaction
ENSG00000257327	Chromatin interaction
ENSG00000138709	Chromatin interaction
ENSG00000120837	Chromatin interaction
ENSG00000188554	Chromatin interaction
ENSG00000237296	Chromatin interaction
ENSG00000188825	Chromatin interaction
ENSG00000181830	Chromatin interaction
ENSG00000214198	Chromatin interaction
ENSG00000159592	Chromatin interaction
ENSG00000159596	Chromatin interaction
ENSG00000139372	Chromatin interaction
ENSG00000140743	Chromatin interaction
ENSG00000141258	Chromatin interaction
ENSG00000204954	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10507170	1.00[ASN][1000 genomes]
rs59681540	0.88[AMR][1000 genomes]
rs60603839	1.00[ASN][1000 genomes]
rs60729918	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61002956	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73177929	0.86[EUR][1000 genomes]
rs73386129	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73386140	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73386143	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73386170	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73386176	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73388209	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73388220	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 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	chr12:104322000-104325000	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr12:104322000-104325200	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr12:104322000-104325200	Active TSS	Rectal Smooth Muscle	rectum
4	chr12:104322200-104324800	Active TSS	Thymus	Thymus
5	chr12:104322200-104325200	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr12:104322200-104325200	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr12:104322200-104326200	Active TSS	H1 Cell Line	embryonic stem cell
8	chr12:104322200-104326200	Active TSS	GM12878-XiMat	blood
9	chr12:104322400-104325200	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr12:104322400-104325200	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr12:104322400-104325200	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr12:104322400-104325400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr12:104322400-104325600	Active TSS	H9 Cell Line	embryonic stem cell
14	chr12:104322400-104325800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr12:104322400-104326000	Active TSS	Colonic Mucosa	Colon
16	chr12:104322400-104326000	Active TSS	Fetal Intestine Small	intestine
17	chr12:104322400-104327000	Active TSS	Right Atrium	heart
18	chr12:104322600-104324800	Active TSS	Primary B cells from peripheral blood	blood
19	chr12:104322600-104325000	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr12:104322600-104325200	Active TSS	Primary T killer memory cells from peripheral blood	blood
21	chr12:104322600-104325200	Active TSS	Brain Substantia Nigra	brain
22	chr12:104322600-104325400	Active TSS	Brain Hippocampus Middle	brain
23	chr12:104322600-104325400	Active TSS	Gastric	stomach
24	chr12:104322600-104325400	Active TSS	Placenta Amnion	Placenta Amnion
25	chr12:104322600-104325600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr12:104322600-104325600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr12:104322600-104325600	Active TSS	Esophagus	oesophagus
28	chr12:104322600-104325600	Active TSS	Sigmoid Colon	Sigmoid Colon
29	chr12:104322600-104325800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr12:104322600-104325800	Active TSS	Fetal Muscle Trunk	muscle
31	chr12:104322600-104326400	Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr12:104322600-104327000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr12:104322600-104327200	Active TSS	Aorta	Aorta
34	chr12:104322800-104324600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
35	chr12:104322800-104324600	Active TSS	Cortex derived primary cultured neurospheres	brain
36	chr12:104322800-104324800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr12:104322800-104325000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr12:104322800-104325000	Active TSS	Primary T helper naive cells from peripheral blood	blood
39	chr12:104322800-104325200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:104322800-104325200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr12:104322800-104325200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr12:104322800-104325200	Active TSS	HUES48 Cell Line	embryonic stem cell
43	chr12:104322800-104325200	Active TSS	Fetal Brain Female	brain
44	chr12:104322800-104325200	Active TSS	Spleen	Spleen
45	chr12:104322800-104325400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr12:104322800-104325400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr12:104322800-104325400	Active TSS	Fetal Kidney	kidney
48	chr12:104322800-104325400	Active TSS	Stomach Mucosa	stomach
49	chr12:104322800-104325400	Bivalent/Poised TSS	HepG2	liver
50	chr12:104322800-104325600	Active TSS	Left Ventricle	heart

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