Variant report

Variant	rs35120599
Chromosome Location	chr9:116173709-116173710
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:53)
CpG islands
(count:0)
Chromatin interactive
region (count:27)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:53 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:116172398-116173875	HCT-116	colon:	n/a	n/a
2	POLR2A	chr9:116172173-116173740	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr9:116172274-116174115	GM18526	blood:	n/a	n/a
4	REST	chr9:116172095-116173731	H1-neurons	neurons:	n/a	chr9:116172729-116172742 chr9:116172827-116172840 chr9:116172825-116172835
5	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
6	POLR2A	chr9:116172172-116173769	K562	blood:	n/a	n/a
7	MAZ	chr9:116171830-116173738	IMR90	lung:	n/a	chr9:116172675-116172690 chr9:116172679-116172688 chr9:116172679-116172688 chr9:116172679-116172689 chr9:116172679-116172688 chr9:116172677-116172686
8	POLR2A	chr9:116173637-116173710	MCF-7	breast:	n/a	n/a
9	CEBPB	chr9:116172286-116173713	K562	blood:	n/a	n/a
10	POLR2A	chr9:116172298-116173849	ProgFib	skin:	n/a	n/a
11	POLR2A	chr9:116173587-116173713	A549	lung:	n/a	n/a
12	POLR2A	chr9:116171966-116173934	GM19193	blood:	n/a	n/a
13	POLR2A	chr9:116172268-116173865	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr9:116171648-116173867	GM12892	blood:	n/a	n/a
15	POLR2A	chr9:116172243-116173911	GM18505	blood:	n/a	n/a
16	POLR2A	chr9:116172152-116173738	MCF-7	breast:	n/a	n/a
17	POLR2A	chr9:116172118-116175047	GM12891	blood:	n/a	n/a
18	POLR2A	chr9:116171826-116173763	GM12878	blood:	n/a	n/a
19	POLR2A	chr9:116171745-116173871	K562	blood:	n/a	n/a
20	POLR2A	chr9:116172343-116173912	GM15510	blood:	n/a	n/a
21	ZNF384	chr9:116172643-116173751	GM12878	blood:	n/a	n/a
22	POLR2A	chr9:116172195-116173709	ECC-1	luminal epithelium:	n/a	n/a
23	POLR2A	chr9:116171883-116173729	IMR90	lung:	n/a	n/a
24	POLR2A	chr9:116172169-116173922	HepG2	liver:	n/a	n/a
25	ZNF384	chr9:116172590-116173888	K562	blood:	n/a	n/a
26	YY1	chr9:116173505-116173721	K562	blood:	n/a	n/a
27	POLR2A	chr9:116171684-116174044	Hela-S3	cervix:	n/a	n/a
28	PML	chr9:116172072-116173760	GM12878	blood:	n/a	n/a
29	POLR2A	chr9:116172300-116173740	K562	blood:	n/a	n/a
30	POLR2A	chr9:116171824-116173812	K562	blood:	n/a	n/a
31	POLR2A	chr9:116172145-116174495	GM18951	blood:	n/a	n/a
32	HCFC1	chr9:116171455-116174137	Hela-S3	cervix:	n/a	n/a
33	MAX	chr9:116172087-116173713	A549	lung:	n/a	chr9:116172675-116172690 chr9:116172679-116172688 chr9:116172679-116172688 chr9:116172679-116172689 chr9:116172679-116172688 chr9:116172677-116172686
34	POLR2A	chr9:116171951-116173895	MCF10A-Er-Src	breast:	n/a	n/a
35	POLR2A	chr9:116172232-116173874	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr9:116171775-116173710	GM12878	blood:	n/a	n/a
37	POLR2A	chr9:116171778-116173836	GM19099	blood:	n/a	n/a
38	POLR2A	chr9:116171686-116173825	K562	blood:	n/a	n/a
39	POLR2A	chr9:116171740-116173833	K562	blood:	n/a	n/a
40	POLR2A	chr9:116172282-116174126	GM12892	blood:	n/a	n/a
41	POLR2A	chr9:116171747-116173975	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr9:116171698-116173713	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr9:116172245-116173760	HUVEC	blood vessel:	n/a	n/a
44	POLR2A	chr9:116172275-116173948	U87	brain:	n/a	n/a
45	HA-E2F1	chr9:116171887-116173998	MCF-7	breast:	n/a	chr9:116172742-116172751
46	POLR2A	chr9:116172134-116174556	Raji	blood:	n/a	n/a
47	POLR2A	chr9:116173688-116173729	GM12878	blood:	n/a	n/a
48	POLR2A	chr9:116172294-116173788	HUVEC	blood vessel:	n/a	n/a
49	POLR2A	chr9:116171726-116173914	SK-N-MC	brain:	n/a	n/a
50	YY1	chr9:116173527-116173749	GM12878	blood:	n/a	n/a

No data

(count:27 , 50 per page) page: 1

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	chr17:56736066..56737863-chr9:116170931..116173878,2	MCF-7	breast:
5	chr9:116037889..116039423-chr9:116171987..116174165,2	MCF-7	breast:
6	chr9:116173439..116175990-chr9:116186543..116189619,3	MCF-7	breast:
7	chr9:116173295..116175149-chr9:116205618..116207587,2	MCF-7	breast:
8	chr9:115981852..115985156-chr9:116171660..116173942,3	MCF-7	breast:
9	chr9:116172702..116174409-chr9:116381360..116383255,2	MCF-7	breast:
10	chr9:116033413..116040476-chr9:116169994..116174441,15	MCF-7	breast:
11	chr9:115980360..115986264-chr9:116170629..116175189,6	K562	blood:
12	chr9:116102456..116104363-chr9:116171276..116174227,4	MCF-7	breast:
13	chr9:116171876..116174337-chr9:116351480..116354219,2	MCF-7	breast:
14	chr9:116171440..116174451-chr9:116224493..116228672,6	MCF-7	breast:
15	chr9:116169791..116174768-chr9:116341586..116346658,6	MCF-7	breast:
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	chr9:116173212..116174744-chr9:116360049..116362132,2	K562	blood:
20	chr9:116035556..116040148-chr9:116171147..116174619,7	K562	blood:
21	chr9:116036437..116039850-chr9:116170281..116174782,6	K562	blood:
22	chr9:116171469..116174533-chr9:116350690..116354091,5	MCF-7	breast:
23	chr9:116063473..116067468-chr9:116171615..116174364,4	MCF-7	breast:
24	chr9:116099899..116105558-chr9:116170913..116174361,7	MCF-7	breast:
25	chr9:116129674..116142040-chr9:116159218..116175468,34	MCF-7	breast:
26	chr9:116060084..116062548-chr9:116172614..116174498,2	K562	blood:
27	chr9:116172568..116175164-chr9:116240650..116243848,4	MCF-7	breast:

No data

Variant related genes	Relation type
POLE3	TF binding region
ENSG00000165188	Chromatin interaction
ENSG00000119321	Chromatin interaction
ENSG00000148225	Chromatin interaction
ENSG00000138835	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000233817	Chromatin interaction
ENSG00000237330	Chromatin interaction
ENSG00000176386	Chromatin interaction
ENSG00000148218	Chromatin interaction
ENSG00000119411	Chromatin interaction
ENSG00000119431	Chromatin interaction
ENSG00000136868	Chromatin interaction
ENSG00000136875	Chromatin interaction
ENSG00000237073	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]
rs17553698	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]
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
rs35120599	RGS3	cis	Whole Blood	GTEx

Chromatin state (count:117 , 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	chr9:116171600-116173800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:116171600-116174000	Active TSS	H9 Cell Line	embryonic stem cell
4	chr9:116171600-116174000	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr9:116171600-116174000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr9:116171600-116174200	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr9:116171600-116174200	Active TSS	Fetal Brain Female	brain
8	chr9:116171800-116173800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr9:116171800-116173800	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr9:116171800-116173800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr9:116171800-116173800	Active TSS	Esophagus	oesophagus
12	chr9:116171800-116174000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr9:116171800-116174000	Active TSS	Psoas Muscle	Psoas
14	chr9:116171800-116174200	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr9:116172000-116173800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr9:116172000-116173800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr9:116172000-116173800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr9:116172000-116173800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr9:116172000-116173800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr9:116172000-116173800	Active TSS	Fetal Muscle Trunk	muscle
21	chr9:116172000-116173800	Active TSS	Left Ventricle	heart
22	chr9:116172000-116173800	Active TSS	A549	lung
23	chr9:116172000-116173800	Active TSS	GM12878-XiMat	blood
24	chr9:116172000-116173800	Active TSS	HSMMtube	muscle
25	chr9:116172000-116173800	Active TSS	NH-A	brain
26	chr9:116172000-116173800	Active TSS	NHLF	lung
27	chr9:116172000-116174000	Active TSS	H1 Cell Line	embryonic stem cell
28	chr9:116172000-116174000	Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr9:116172000-116174000	Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr9:116172000-116174000	Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr9:116172000-116174000	Active TSS	Fetal Intestine Large	intestine
32	chr9:116172000-116174000	Active TSS	Fetal Kidney	kidney
33	chr9:116172000-116174000	Active TSS	Ovary	ovary
34	chr9:116172000-116174000	Active TSS	Placenta Amnion	Placenta Amnion
35	chr9:116172000-116174000	Active TSS	NHEK	skin
36	chr9:116172000-116174200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr9:116172000-116174200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr9:116172000-116174200	Active TSS	HUES64 Cell Line	embryonic stem cell
39	chr9:116172000-116174200	Active TSS	Brain Germinal Matrix	brain
40	chr9:116172200-116173800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr9:116172200-116173800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr9:116172200-116173800	Active TSS	Primary hematopoietic stem cells short term culture	blood
43	chr9:116172200-116173800	Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr9:116172200-116173800	Active TSS	Muscle Satellite Cultured Cells	--
45	chr9:116172200-116173800	Active TSS	Brain Anterior Caudate	brain
46	chr9:116172200-116173800	Active TSS	Brain Hippocampus Middle	brain
47	chr9:116172200-116173800	Active TSS	Colon Smooth Muscle	Colon
48	chr9:116172200-116173800	Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr9:116172200-116173800	Active TSS	Fetal Intestine Small	intestine
50	chr9:116172200-116173800	Active TSS	Fetal Lung	lung

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