Variant report

Variant	rs34142167
Chromosome Location	chr9:116173983-116173984
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:25)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:116172274-116174115	GM18526	blood:	n/a	n/a
2	POLR2A	chr9:116172118-116175047	GM12891	blood:	n/a	n/a
3	POLR2A	chr9:116171684-116174044	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr9:116172145-116174495	GM18951	blood:	n/a	n/a
5	HCFC1	chr9:116171455-116174137	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr9:116172282-116174126	GM12892	blood:	n/a	n/a
7	HA-E2F1	chr9:116171887-116173998	MCF-7	breast:	n/a	chr9:116172742-116172751
8	POLR2A	chr9:116172134-116174556	Raji	blood:	n/a	n/a
9	POLR2A	chr9:116173975-116174549	HepG2	liver:	n/a	n/a
10	CHD1	chr9:116172279-116174071	H1-hESC	embryonic stem cell:	n/a	chr9:116172727-116172737

No data

(count:25 , 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	chr9:116037889..116039423-chr9:116171987..116174165,2	MCF-7	breast:
5	chr9:116173439..116175990-chr9:116186543..116189619,3	MCF-7	breast:
6	chr9:116173295..116175149-chr9:116205618..116207587,2	MCF-7	breast:
7	chr9:116172702..116174409-chr9:116381360..116383255,2	MCF-7	breast:
8	chr9:116033413..116040476-chr9:116169994..116174441,15	MCF-7	breast:
9	chr9:115980360..115986264-chr9:116170629..116175189,6	K562	blood:
10	chr9:116102456..116104363-chr9:116171276..116174227,4	MCF-7	breast:
11	chr9:116171876..116174337-chr9:116351480..116354219,2	MCF-7	breast:
12	chr9:116171440..116174451-chr9:116224493..116228672,6	MCF-7	breast:
13	chr9:116169791..116174768-chr9:116341586..116346658,6	MCF-7	breast:
14	chr9:116110213..116113414-chr9:116171126..116174421,5	MCF-7	breast:
15	chr9:116162231..116166322-chr9:116170436..116174778,10	MCF-7	breast:
16	chr9:116172469..116174359-chr9:116325229..116328003,2	K562	blood:
17	chr9:116173212..116174744-chr9:116360049..116362132,2	K562	blood:
18	chr9:116035556..116040148-chr9:116171147..116174619,7	K562	blood:
19	chr9:116036437..116039850-chr9:116170281..116174782,6	K562	blood:
20	chr9:116171469..116174533-chr9:116350690..116354091,5	MCF-7	breast:
21	chr9:116063473..116067468-chr9:116171615..116174364,4	MCF-7	breast:
22	chr9:116099899..116105558-chr9:116170913..116174361,7	MCF-7	breast:
23	chr9:116129674..116142040-chr9:116159218..116175468,34	MCF-7	breast:
24	chr9:116060084..116062548-chr9:116172614..116174498,2	K562	blood:
25	chr9:116172568..116175164-chr9:116240650..116243848,4	MCF-7	breast:

No data

Variant related genes	Relation type
POLE3	TF binding region
ENSG00000148218	Chromatin interaction
ENSG00000148225	Chromatin interaction
ENSG00000136875	Chromatin interaction
ENSG00000138835	Chromatin interaction
ENSG00000165188	Chromatin interaction
ENSG00000233817	Chromatin interaction
ENSG00000237330	Chromatin interaction
ENSG00000119321	Chromatin interaction
ENSG00000176386	Chromatin interaction
ENSG00000136868	Chromatin interaction
ENSG00000119411	Chromatin interaction
ENSG00000119431	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]
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
rs34142167	RGS3	cis	Whole Blood	GTEx

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116171400-116174200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr9:116171600-116174000	Active TSS	H9 Cell Line	embryonic stem cell
3	chr9:116171600-116174000	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr9:116171600-116174000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr9:116171600-116174200	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr9:116171600-116174200	Active TSS	Fetal Brain Female	brain
7	chr9:116171800-116174000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr9:116171800-116174000	Active TSS	Psoas Muscle	Psoas
9	chr9:116171800-116174200	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr9:116172000-116174000	Active TSS	H1 Cell Line	embryonic stem cell
11	chr9:116172000-116174000	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr9:116172000-116174000	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr9:116172000-116174000	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr9:116172000-116174000	Active TSS	Fetal Intestine Large	intestine
15	chr9:116172000-116174000	Active TSS	Fetal Kidney	kidney
16	chr9:116172000-116174000	Active TSS	Ovary	ovary
17	chr9:116172000-116174000	Active TSS	Placenta Amnion	Placenta Amnion
18	chr9:116172000-116174000	Active TSS	NHEK	skin
19	chr9:116172000-116174200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr9:116172000-116174200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr9:116172000-116174200	Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr9:116172000-116174200	Active TSS	Brain Germinal Matrix	brain
23	chr9:116172200-116174000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr9:116172200-116174000	Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr9:116172200-116174000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr9:116172200-116174000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr9:116172200-116174000	Active TSS	Aorta	Aorta
28	chr9:116172200-116174000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr9:116172200-116174000	Active TSS	Colonic Mucosa	Colon
30	chr9:116172200-116174000	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr9:116172200-116174000	Active TSS	Fetal Stomach	stomach
32	chr9:116172200-116174000	Active TSS	Thymus	Thymus
33	chr9:116172200-116174000	Active TSS	Dnd41	blood
34	chr9:116172200-116174000	Active TSS	Hela-S3	cervix
35	chr9:116172200-116174000	Active TSS	HMEC	breast
36	chr9:116172200-116174000	Active TSS	HSMM	muscle
37	chr9:116172200-116174000	Active TSS	HUVEC	blood vessel
38	chr9:116172200-116174000	Active TSS	K562	blood
39	chr9:116172200-116174000	Active TSS	NHDF-Ad	bronchial
40	chr9:116172200-116174000	Active TSS	Osteobl	bone
41	chr9:116172200-116174200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr9:116172200-116174200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr9:116172200-116174200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr9:116172400-116174000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
45	chr9:116172400-116174000	Active TSS	Liver	Liver
46	chr9:116172400-116174000	Active TSS	Brain Angular Gyrus	brain
47	chr9:116172400-116174000	Active TSS	Brain Inferior Temporal Lobe	brain
48	chr9:116172400-116174000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
49	chr9:116172400-116174000	Active TSS	Rectal Mucosa Donor 29	rectum
50	chr9:116172400-116174000	Active TSS	Right Ventricle	heart

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