Variant report

Variant	rs17553698
Chromosome Location	chr9:116173181-116173182
allele	A/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	EGR1	chr9:116172299-116173283	MCF-7	breast:	n/a	chr9:116172744-116172755 chr9:116172741-116172751 chr9:116172743-116172756
2	EGR1	chr9:116172405-116173279	ECC-1	luminal epithelium:	n/a	chr9:116172744-116172755 chr9:116172741-116172751 chr9:116172743-116172756
3	CEBPB	chr9:116172447-116173578	GM12878	blood:	n/a	n/a
4	E2F6	chr9:116172214-116173285	H1-hESC	embryonic stem cell:	n/a	chr9:116172632-116172643 chr9:116172742-116172751
5	ETS1	chr9:116172343-116173309	A549	lung:	n/a	chr9:116172745-116172756
6	POLR2A	chr9:116172110-116173588	PBDE	blood:	n/a	n/a
7	GATA3	chr9:116172310-116173577	MCF-7	breast:	n/a	n/a
8	TCF7L2	chr9:116172466-116173236	HCT-116	colon:	n/a	n/a
9	MAZ	chr9:116171928-116173474	K562	blood:	n/a	chr9:116172675-116172690 chr9:116172679-116172688 chr9:116172679-116172688 chr9:116172679-116172689 chr9:116172679-116172688 chr9:116172677-116172686
10	POLR2A	chr9:116171707-116173648	HL-60	blood:	n/a	n/a
11	PBX3	chr9:116172214-116173272	A549	lung:	n/a	n/a
12	EP300	chr9:116172469-116173421	GM12878	blood:	n/a	chr9:116173173-116173187
13	MAFF	chr9:116172584-116173206	HepG2	liver:	n/a	n/a
14	REST	chr9:116172243-116173659	A549	lung:	n/a	chr9:116172729-116172742 chr9:116172827-116172840 chr9:116172825-116172835
15	POLR2A	chr9:116172356-116173515	HepG2	liver:	n/a	n/a
16	SIN3AK20	chr9:116172189-116173310	SK-N-SH	brain:	n/a	n/a
17	POLR2A	chr9:116172282-116173236	MCF-7	breast:	n/a	n/a
18	MYC	chr9:116172264-116173189	MCF-7	breast:	n/a	chr9:116172675-116172690 chr9:116172679-116172688 chr9:116172679-116172688 chr9:116172679-116172689 chr9:116172679-116172688 chr9:116172677-116172686
19	STAT5A	chr9:116172401-116173484	K562	blood:	n/a	chr9:116173191-116173200 chr9:116173177-116173188 chr9:116172665-116172676 chr9:116173190-116173199
20	CREB1	chr9:116172534-116173218	A549	lung:	n/a	n/a
21	TBP	chr9:116172239-116173497	H1-hESC	embryonic stem cell:	n/a	n/a
22	RUNX3	chr9:116172353-116173537	GM12878	blood:	n/a	n/a
23	NR3C1	chr9:116172415-116173182	A549	lung:	n/a	n/a
24	POU2F2	chr9:116172319-116173263	GM12878	blood:	n/a	chr9:116172733-116172745
25	POLR2A	chr9:116172403-116173267	HepG2	liver:	n/a	n/a
26	POLR2A	chr9:116172398-116173875	HCT-116	colon:	n/a	n/a
27	POLR2A	chr9:116172173-116173740	Hela-S3	cervix:	n/a	n/a
28	BRCA1	chr9:116172444-116173239	HepG2	liver:	n/a	n/a
29	CEBPD	chr9:116172484-116173238	HepG2	liver:	n/a	n/a
30	POLR2A	chr9:116172274-116174115	GM18526	blood:	n/a	n/a
31	SP1	chr9:116172408-116173347	GM12878	blood:	n/a	chr9:116172838-116172847 chr9:116172740-116172752 chr9:116172742-116172751 chr9:116172723-116172737 chr9:116172741-116172750 chr9:116172740-116172752
32	POLR2A	chr9:116172255-116173497	H1-hESC	embryonic stem cell:	n/a	n/a
33	TAF1	chr9:116172263-116173579	A549	lung:	n/a	n/a
34	REST	chr9:116172095-116173731	H1-neurons	neurons:	n/a	chr9:116172729-116172742 chr9:116172827-116172840 chr9:116172825-116172835
35	YY1	chr9:116172180-116173201	K562	blood:	n/a	chr9:116172957-116172971 chr9:116172745-116172754
36	POLR2A	chr9:116172375-116173552	U87	brain:	n/a	n/a
37	MAFK	chr9:116172841-116173416	H1-hESC	embryonic stem cell:	n/a	n/a
38	TBP	chr9:116171856-116173535	K562	blood:	n/a	n/a
39	REST	chr9:116172893-116173237	K562	blood:	n/a	n/a
40	TAL1	chr9:116172496-116173535	K562	blood:	n/a	n/a
41	TAF1	chr9:116172284-116173310	GM12878	blood:	n/a	n/a
42	SIN3AK20	chr9:116172169-116173207	H1-hESC	embryonic stem cell:	n/a	n/a
43	SMARCB1	chr9:116172004-116173200	Hela-S3	cervix:	n/a	n/a
44	MYC	chr9:116172113-116173816	K562	blood:	n/a	chr9:116172675-116172690 chr9:116172679-116172688 chr9:116172679-116172688 chr9:116172679-116172689 chr9:116172679-116172688 chr9:116172677-116172686
45	RCOR1	chr9:116172249-116173427	K562	blood:	n/a	n/a
46	CBX3	chr9:116172554-116173384	K562	blood:	n/a	n/a
47	SIN3A	chr9:116172106-116173392	GM12878	blood:	n/a	chr9:116172680-116172689 chr9:116172732-116172745 chr9:116172966-116172977
48	POLR2A	chr9:116172172-116173769	K562	blood:	n/a	n/a
49	POLR2A	chr9:116172286-116173201	A549	lung:	n/a	n/a
50	RFX5	chr9:116172428-116173453	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:116135295..116143276-chr9:116169551..116176415,12	MCF-7	breast:
2	chr9:116171540..116174931-chr9:116223597..116227370,5	MCF-7	breast:
3	chr1:1008774..1011772-chr9:116172716..116174987,2	MCF-7	breast:
4	chr9:116137731..116139998-chr9:116170716..116173211,2	K562	blood:
5	chr17:56736066..56737863-chr9:116170931..116173878,2	MCF-7	breast:
6	chr9:116037889..116039423-chr9:116171987..116174165,2	MCF-7	breast:
7	chr9:115981852..115985156-chr9:116171660..116173942,3	MCF-7	breast:
8	chr9:116172702..116174409-chr9:116381360..116383255,2	MCF-7	breast:
9	chr9:116033413..116040476-chr9:116169994..116174441,15	MCF-7	breast:
10	chr9:115980360..115986264-chr9:116170629..116175189,6	K562	blood:
11	chr9:116102456..116104363-chr9:116171276..116174227,4	MCF-7	breast:
12	chr9:116171876..116174337-chr9:116351480..116354219,2	MCF-7	breast:
13	chr9:116171440..116174451-chr9:116224493..116228672,6	MCF-7	breast:
14	chr9:116169791..116174768-chr9:116341586..116346658,6	MCF-7	breast:
15	chr17:45400573..45401426-chr9:116172200..116173194,2	Hela-S3	cervix:
16	chr9:116110213..116113414-chr9:116171126..116174421,5	MCF-7	breast:
17	chr9:116162231..116166322-chr9:116170436..116174778,10	MCF-7	breast:
18	chr9:116172469..116174359-chr9:116325229..116328003,2	K562	blood:
19	chr9:116035556..116040148-chr9:116171147..116174619,7	K562	blood:
20	chr9:116036437..116039850-chr9:116170281..116174782,6	K562	blood:
21	chr9:116171469..116174533-chr9:116350690..116354091,5	MCF-7	breast:
22	chr9:116137711..116140473-chr9:116169496..116173211,3	K562	blood:
23	chr9:116063473..116067468-chr9:116171615..116174364,4	MCF-7	breast:
24	chr9:4679491..4679999-chr9:116172684..116173519,2	NB4	blood:
25	chr9:116099899..116105558-chr9:116170913..116174361,7	MCF-7	breast:
26	chr9:116129674..116142040-chr9:116159218..116175468,34	MCF-7	breast:
27	chr9:116060084..116062548-chr9:116172614..116174498,2	K562	blood:
28	chr9:116172568..116175164-chr9:116240650..116243848,4	MCF-7	breast:
29	chr11:33757522..33758216-chr9:116172881..116173475,2	Hela-S3	cervix:

Variant related genes	Relation type
POLE3	TF binding region
ENSG00000178852	Chromatin interaction
ENSG00000148218	Chromatin interaction
ENSG00000106993	Chromatin interaction
ENSG00000119411	Chromatin interaction
ENSG00000148225	Chromatin interaction
ENSG00000237330	Chromatin interaction
ENSG00000119321	Chromatin interaction
ENSG00000165188	Chromatin interaction
ENSG00000085063	Chromatin interaction
ENSG00000136868	Chromatin interaction
ENSG00000119431	Chromatin interaction
ENSG00000237073	Chromatin interaction
ENSG00000138835	Chromatin interaction
ENSG00000136875	Chromatin interaction
ENSG00000273061	Chromatin interaction
ENSG00000263293	Chromatin interaction
ENSG00000176386	Chromatin interaction
ENSG00000233817	Chromatin interaction
ENSG00000202077	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10981793	1.00[ASN][1000 genomes]
rs12338788	1.00[ASN][1000 genomes]
rs12347382	0.86[ASN][1000 genomes]
rs12351728	0.86[ASN][1000 genomes]
rs17525042	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34106027	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34142167	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35081798	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35120599	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35329679	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3747813	0.97[EUR][1000 genomes]
rs3761819	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3810925	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3810926	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3827674	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41276809	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41276823	0.90[EUR][1000 genomes]
rs41306506	0.97[EUR][1000 genomes]
rs41312200	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41316948	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55714377	0.86[ASN][1000 genomes]
rs7042968	1.00[ASN][1000 genomes]
rs72760096	1.00[ASN][1000 genomes]
rs72761906	0.86[ASN][1000 genomes]
rs72761963	0.86[ASN][1000 genomes]
rs72761965	0.86[ASN][1000 genomes]
rs7852118	0.86[ASN][1000 genomes]
rs7855434	0.86[ASN][1000 genomes]
rs7856689	1.00[ASN][1000 genomes]
rs7857217	0.86[ASN][1000 genomes]
rs7864467	0.86[ASN][1000 genomes]
rs7864816	1.00[ASN][1000 genomes]
rs7870142	0.86[ASN][1000 genomes]
rs7870912	0.86[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	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17553698	RGS3	cis	Whole Blood	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116171400-116174200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr9:116171600-116173400	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
3	chr9:116171600-116173800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr9:116171600-116174000	Active TSS	H9 Cell Line	embryonic stem cell
5	chr9:116171600-116174000	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr9:116171600-116174000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr9:116171600-116174200	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr9:116171600-116174200	Active TSS	Fetal Brain Female	brain
9	chr9:116171800-116173400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
10	chr9:116171800-116173600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
11	chr9:116171800-116173800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr9:116171800-116173800	Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr9:116171800-116173800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr9:116171800-116173800	Active TSS	Esophagus	oesophagus
15	chr9:116171800-116174000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr9:116171800-116174000	Active TSS	Psoas Muscle	Psoas
17	chr9:116171800-116174200	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr9:116172000-116173600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr9:116172000-116173600	Active TSS	Primary T killer memory cells from peripheral blood	blood
20	chr9:116172000-116173600	Active TSS	Gastric	stomach
21	chr9:116172000-116173600	Bivalent/Poised TSS	HepG2	liver
22	chr9:116172000-116173800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr9:116172000-116173800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr9:116172000-116173800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr9:116172000-116173800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr9:116172000-116173800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr9:116172000-116173800	Active TSS	Fetal Muscle Trunk	muscle
28	chr9:116172000-116173800	Active TSS	Left Ventricle	heart
29	chr9:116172000-116173800	Active TSS	A549	lung
30	chr9:116172000-116173800	Active TSS	GM12878-XiMat	blood
31	chr9:116172000-116173800	Active TSS	HSMMtube	muscle
32	chr9:116172000-116173800	Active TSS	NH-A	brain
33	chr9:116172000-116173800	Active TSS	NHLF	lung
34	chr9:116172000-116174000	Active TSS	H1 Cell Line	embryonic stem cell
35	chr9:116172000-116174000	Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr9:116172000-116174000	Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr9:116172000-116174000	Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr9:116172000-116174000	Active TSS	Fetal Intestine Large	intestine
39	chr9:116172000-116174000	Active TSS	Fetal Kidney	kidney
40	chr9:116172000-116174000	Active TSS	Ovary	ovary
41	chr9:116172000-116174000	Active TSS	Placenta Amnion	Placenta Amnion
42	chr9:116172000-116174000	Active TSS	NHEK	skin
43	chr9:116172000-116174200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
44	chr9:116172000-116174200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr9:116172000-116174200	Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr9:116172000-116174200	Active TSS	Brain Germinal Matrix	brain
47	chr9:116172200-116173200	Transcr. at gene 5' and 3'	Right Atrium	heart
48	chr9:116172200-116173600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr9:116172200-116173600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr9:116172200-116173600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood

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