Variant report

Variant	rs3827674
Chromosome Location	chr9:116171275-116171276
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:116135295..116143276-chr9:116169551..116176415,12	MCF-7	breast:
2	chr9:116137731..116139998-chr9:116170716..116173211,2	K562	blood:
3	chr17:56736066..56737863-chr9:116170931..116173878,2	MCF-7	breast:
4	chr9:116033413..116040476-chr9:116169994..116174441,15	MCF-7	breast:
5	chr9:116116941..116119780-chr9:116168101..116172088,3	MCF-7	breast:
6	chr9:115983607..115986374-chr9:116170251..116172763,3	MCF-7	breast:
7	chr9:115980360..115986264-chr9:116170629..116175189,6	K562	blood:
8	chr2:196521632..196523529-chr9:116170314..116172766,2	MCF-7	breast:
9	chr9:116171144..116172776-chr9:116342569..116344666,2	MCF-7	breast:
10	chr9:116169791..116174768-chr9:116341586..116346658,6	MCF-7	breast:
11	chr9:116110213..116113414-chr9:116171126..116174421,5	MCF-7	breast:
12	chr9:116162231..116166322-chr9:116170436..116174778,10	MCF-7	breast:
13	chr9:116035556..116040148-chr9:116171147..116174619,7	K562	blood:
14	chr9:116035649..116038328-chr9:116169495..116171844,3	MCF-7	breast:
15	chr9:116036437..116039850-chr9:116170281..116174782,6	K562	blood:
16	chr9:116137711..116140473-chr9:116169496..116173211,3	K562	blood:
17	chr9:116099899..116105558-chr9:116170913..116174361,7	MCF-7	breast:
18	chr9:116129674..116142040-chr9:116159218..116175468,34	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000136875	Chromatin interaction
ENSG00000138835	Chromatin interaction
ENSG00000176386	Chromatin interaction
ENSG00000148218	Chromatin interaction
ENSG00000119431	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000119321	Chromatin interaction
ENSG00000119411	Chromatin interaction
ENSG00000136868	Chromatin interaction
ENSG00000148225	Chromatin interaction
ENSG00000196950	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10981793	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10981815	1.00[CHB][hapmap]
rs12338788	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12347382	0.86[ASN][1000 genomes]
rs12351728	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs17525042	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17553698	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2761025	1.00[CHD][hapmap]
rs2792818	1.00[CHD][hapmap]
rs34106027	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34142167	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35081798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35120599	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35329679	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3747813	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs3761819	1.00[CHB][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3810925	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3810926	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41276809	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[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41316948	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55714377	0.86[ASN][1000 genomes]
rs7042968	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7049221	1.00[CHB][hapmap]
rs72760096	1.00[ASN][1000 genomes]
rs72761906	0.86[ASN][1000 genomes]
rs72761963	0.86[ASN][1000 genomes]
rs72761965	0.86[ASN][1000 genomes]
rs7851937	1.00[CHB][hapmap]
rs7852118	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs7854524	1.00[CHB][hapmap]
rs7855434	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs7856689	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7857217	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs7864467	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs7864816	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7870142	0.86[ASN][1000 genomes]
rs7870912	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs883025	1.00[CHB][hapmap]
rs884898	1.00[CHB][hapmap]
rs9785299	1.00[CHB][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3827674	POLE3	cis	lymphoblastoid	seeQTL
rs3827674	RGS3	cis	Whole Blood	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116163600-116172200	Weak transcription	Small Intestine	intestine
2	chr9:116164000-116171400	Weak transcription	Pancreas	Pancrea
3	chr9:116164000-116171600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr9:116164000-116171600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr9:116164200-116171800	Weak transcription	Right Atrium	heart
6	chr9:116164200-116172000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr9:116164400-116171600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr9:116164400-116171600	Weak transcription	Colonic Mucosa	Colon
9	chr9:116164400-116171600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr9:116164400-116171800	Weak transcription	Stomach Mucosa	stomach
11	chr9:116167400-116171400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr9:116169200-116171600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
13	chr9:116169200-116171600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr9:116169400-116171400	Strong transcription	H9 Cell Line	embryonic stem cell
15	chr9:116169400-116171400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr9:116169400-116171400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr9:116169400-116171400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr9:116169400-116171400	Genic enhancers	NHEK	skin
19	chr9:116169400-116171600	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr9:116169400-116171600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr9:116169400-116171600	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr9:116169400-116171600	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr9:116169400-116171600	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr9:116169400-116171600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr9:116169400-116171600	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr9:116169400-116171600	Strong transcription	Placenta	Placenta
27	chr9:116169400-116171600	Strong transcription	HSMM	muscle
28	chr9:116169600-116171400	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr9:116169600-116171400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr9:116169600-116171400	Strong transcription	Brain Cingulate Gyrus	brain
31	chr9:116169600-116171400	Weak transcription	Fetal Heart	heart
32	chr9:116169600-116171600	Strong transcription	HSMMtube	muscle
33	chr9:116169600-116171800	Genic enhancers	Primary T cells fromperipheralblood	blood
34	chr9:116169800-116171400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr9:116169800-116171400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr9:116169800-116171400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr9:116169800-116171400	Strong transcription	Primary B cells from peripheral blood	blood
38	chr9:116169800-116171400	Strong transcription	Fetal Muscle Trunk	muscle
39	chr9:116169800-116171400	Strong transcription	Gastric	stomach
40	chr9:116169800-116171400	Strong transcription	Thymus	Thymus
41	chr9:116169800-116171600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
42	chr9:116169800-116171600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr9:116169800-116171600	Strong transcription	Fetal Intestine Small	intestine
44	chr9:116169800-116171800	Strong transcription	Lung	lung
45	chr9:116169800-116171800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
46	chr9:116170000-116171400	Genic enhancers	Primary T cells from cord blood	blood
47	chr9:116170000-116171400	Strong transcription	Left Ventricle	heart
48	chr9:116170000-116171400	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr9:116170000-116171600	Strong transcription	Fetal Stomach	stomach
50	chr9:116170000-116171600	Strong transcription	Skeletal Muscle Male	skeletal muscle

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