Variant report

Variant	rs55714377
Chromosome Location	chr9:116274934-116274935
allele	G/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	BCLAF1	chr9:116274261-116275080	GM12878	blood:	n/a	chr9:116274694-116274703
2	POU2F2	chr9:116274518-116274949	GM12878	blood:	n/a	n/a
3	TCF3	chr9:116274641-116274987	GM12878	blood:	n/a	chr9:116274927-116274937
4	BCL11A	chr9:116274562-116275023	GM12878	blood:	n/a	chr9:116274694-116274703
5	EBF1	chr9:116274449-116275274	GM12878	blood:	n/a	n/a
6	RELA	chr9:116274255-116275144	GM18951	blood:	n/a	n/a
7	PAX5	chr9:116274539-116275056	GM12878	blood:	n/a	chr9:116274694-116274703
8	SP1	chr9:116274486-116275101	GM12878	blood:	n/a	chr9:116274817-116274831
9	ELF1	chr9:116274600-116275178	GM12878	blood:	n/a	n/a
10	CHD1	chr9:116274265-116275051	GM12878	blood:	n/a	n/a
11	RELA	chr9:116274213-116275106	GM15510	blood:	n/a	n/a
12	MTA3	chr9:116274236-116275229	GM12878	blood:	n/a	n/a
13	POU2F2	chr9:116274470-116275111	GM12891	blood:	n/a	chr9:116275097-116275109
14	RUNX3	chr9:116274294-116275257	GM12878	blood:	n/a	n/a
15	MTA3	chr9:116273986-116275187	GM12878	blood:	n/a	n/a
16	TCF12	chr9:116274624-116275134	GM12878	blood:	n/a	chr9:116274952-116274962
17	CHD2	chr9:116274502-116275159	GM12878	blood:	n/a	n/a
18	FOXM1	chr9:116274485-116275093	GM12878	blood:	n/a	n/a
19	RELA	chr9:116274280-116275118	GM18505	blood:	n/a	n/a
20	EP300	chr9:116274547-116275048	GM12878	blood:	n/a	n/a
21	BATF	chr9:116274449-116275045	GM12878	blood:	n/a	n/a
22	MAZ	chr9:116274507-116275079	GM12878	blood:	n/a	n/a
23	YY1	chr9:116274535-116274969	GM12878	blood:	n/a	n/a
24	ELK1	chr9:116274517-116275044	GM12878	blood:	n/a	n/a
25	MYC	chr9:116274508-116275024	NB4	blood:	n/a	n/a
26	CEBPB	chr9:116274801-116274989	GM12878	blood:	n/a	n/a
27	TBL1XR1	chr9:116274439-116275120	GM12878	blood:	n/a	n/a
28	BCL11A	chr9:116274471-116275111	GM12878	blood:	n/a	chr9:116274694-116274703 chr9:116275090-116275099
29	POLR2A	chr9:116274601-116274984	HUVEC	blood vessel:	n/a	n/a
30	NRF1	chr9:116274539-116275019	GM12878	blood:	n/a	n/a
31	NFIC	chr9:116274417-116275108	GM12878	blood:	n/a	n/a
32	POLR2A	chr9:116274383-116275135	GM12892	blood:	n/a	n/a
33	BHLHE40	chr9:116274336-116275115	GM12878	blood:	n/a	n/a
34	BCLAF1	chr9:116274254-116275091	GM12878	blood:	n/a	chr9:116274694-116274703
35	STAT5A	chr9:116274507-116275183	GM12878	blood:	n/a	chr9:116274692-116274700
36	RELA	chr9:116274243-116275201	GM19193	blood:	n/a	n/a
37	RCOR1	chr9:116274294-116275077	GM12878	blood:	n/a	n/a
38	POU2F2	chr9:116274408-116275062	GM12891	blood:	n/a	n/a
39	ATF2	chr9:116274404-116275122	GM12878	blood:	n/a	n/a
40	ZEB1	chr9:116274615-116275195	GM12878	blood:	n/a	n/a
41	EP300	chr9:116274435-116275112	GM12878	blood:	n/a	n/a
42	NFATC1	chr9:116274432-116275067	GM12878	blood:	n/a	n/a
43	RELA	chr9:116274403-116275125	GM10847	blood:	n/a	n/a
44	FOXM1	chr9:116274368-116275145	GM12878	blood:	n/a	n/a
45	RELA	chr9:116274247-116275121	GM19099	blood:	n/a	n/a
46	POLR2A	chr9:116274295-116274944	GM12892	blood:	n/a	n/a
47	EGR1	chr9:116274675-116275009	GM12878	blood:	n/a	chr9:116274694-116274703 chr9:116274817-116274831
48	STAT5A	chr9:116274380-116275174	GM12878	blood:	n/a	chr9:116274692-116274700
49	ATF2	chr9:116274362-116274991	GM12878	blood:	n/a	n/a
50	ZNF143	chr9:116274641-116275053	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:116274772..116276369-chr9:116340475..116342047,2	MCF-7	breast:
2	chr9:116268020..116270746-chr9:116274035..116276805,2	MCF-7	breast:

Variant related genes	Relation type
RGS3	TF binding region

Extended variants
information (count: 183 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:178)

rs_ID	r²[population]
rs10125960	0.91[AFR][1000 genomes]
rs10217237	0.91[AFR][1000 genomes]
rs10217750	0.91[AFR][1000 genomes]
rs10217756	0.91[AFR][1000 genomes]
rs10481640	0.91[AFR][1000 genomes]
rs10481676	0.91[AFR][1000 genomes]
rs10481677	0.87[AFR][1000 genomes]
rs10981793	0.94[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10981794	0.94[AFR][1000 genomes]
rs10981803	0.89[AFR][1000 genomes]
rs10981807	0.85[AFR][1000 genomes]
rs10981808	0.85[AFR][1000 genomes]
rs10981814	0.85[AFR][1000 genomes]
rs10981815	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10981816	0.85[AFR][1000 genomes]
rs10981817	0.85[AFR][1000 genomes]
rs10981819	0.86[AFR][1000 genomes]
rs10981820	0.85[AFR][1000 genomes]
rs10981821	0.85[AFR][1000 genomes]
rs10981825	0.83[AFR][1000 genomes]
rs10981826	0.83[AFR][1000 genomes]
rs10981827	0.83[AFR][1000 genomes]
rs10981830	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10981832	0.83[AFR][1000 genomes]
rs12335991	0.91[AFR][1000 genomes]
rs12336719	0.89[AFR][1000 genomes]
rs12337340	0.81[AFR][1000 genomes]
rs12338221	0.90[AFR][1000 genomes]
rs12338588	0.85[AFR][1000 genomes]
rs12338697	0.81[AFR][1000 genomes]
rs12338701	0.81[AFR][1000 genomes]
rs12338788	0.82[AFR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12339493	0.82[AFR][1000 genomes]
rs12339617	0.86[AFR][1000 genomes]
rs12339851	0.91[AFR][1000 genomes]
rs12340996	0.89[AFR][1000 genomes]
rs12342508	0.91[AFR][1000 genomes]
rs12342699	0.84[AFR][1000 genomes]
rs12343141	0.85[AFR][1000 genomes]
rs12344334	0.83[AFR][1000 genomes]
rs12344578	0.85[AFR][1000 genomes]
rs12344964	0.91[AFR][1000 genomes]
rs12345524	0.85[AFR][1000 genomes]
rs12346076	0.85[AFR][1000 genomes]
rs12346087	0.82[AFR][1000 genomes]
rs12346939	0.91[AFR][1000 genomes]
rs12347382	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12347895	0.82[AFR][1000 genomes]
rs12351728	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17187621	0.83[EUR][1000 genomes]
rs17525042	0.86[ASN][1000 genomes]
rs17553698	0.86[ASN][1000 genomes]
rs1890992	0.83[AFR][1000 genomes]
rs2050865	0.89[AFR][1000 genomes]
rs2050866	0.89[AFR][1000 genomes]
rs28694002	0.85[AFR][1000 genomes]
rs28709996	0.91[AFR][1000 genomes]
rs28714985	0.85[AFR][1000 genomes]
rs34106027	0.86[ASN][1000 genomes]
rs34142167	0.86[ASN][1000 genomes]
rs35120599	0.86[ASN][1000 genomes]
rs35270441	0.89[AFR][1000 genomes]
rs35329679	0.86[ASN][1000 genomes]
rs3761819	0.86[ASN][1000 genomes]
rs3810925	0.86[ASN][1000 genomes]
rs3810926	0.86[ASN][1000 genomes]
rs3827674	0.86[ASN][1000 genomes]
rs3983381	0.83[AFR][1000 genomes]
rs41276809	0.86[ASN][1000 genomes]
rs41301525	0.82[AFR][1000 genomes]
rs41305473	0.82[AFR][1000 genomes]
rs41312200	0.86[ASN][1000 genomes]
rs41316948	0.86[ASN][1000 genomes]
rs4596719	0.89[AFR][1000 genomes]
rs55676913	0.91[AFR][1000 genomes]
rs55777057	0.83[AFR][1000 genomes]
rs55931715	0.83[AFR][1000 genomes]
rs55977108	0.85[AFR][1000 genomes]
rs56155263	0.82[AFR][1000 genomes]
rs56276438	0.83[AFR][1000 genomes]
rs56390346	0.83[AFR][1000 genomes]
rs6478011	0.91[AFR][1000 genomes]
rs6478016	0.91[AFR][1000 genomes]
rs6478017	0.91[AFR][1000 genomes]
rs6478022	0.83[AFR][1000 genomes]
rs6478023	0.83[AFR][1000 genomes]
rs7018783	0.85[AFR][1000 genomes]
rs7020623	0.91[AFR][1000 genomes]
rs7021491	0.91[AFR][1000 genomes]
rs7023661	0.91[AFR][1000 genomes]
rs7024445	0.83[AFR][1000 genomes]
rs7024612	0.83[AFR][1000 genomes]
rs7024996	0.82[AFR][1000 genomes]
rs7025170	0.83[AFR][1000 genomes]
rs7025745	0.85[AFR][1000 genomes]
rs7026568	0.89[AFR][1000 genomes]
rs7026656	0.89[AFR][1000 genomes]
rs7027024	0.89[AFR][1000 genomes]
rs7027340	0.91[AFR][1000 genomes]
rs7028327	0.91[AFR][1000 genomes]
rs7029685	0.85[AFR][1000 genomes]
rs7033679	0.91[AFR][1000 genomes]
rs7037441	0.85[AFR][1000 genomes]
rs7037761	0.92[AFR][1000 genomes]
rs7040031	0.91[AFR][1000 genomes]
rs7040635	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7042290	0.91[AFR][1000 genomes]
rs7042695	0.85[AFR][1000 genomes]
rs7042968	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7043140	0.89[AFR][1000 genomes]
rs7045347	0.91[AFR][1000 genomes]
rs7046202	0.91[AFR][1000 genomes]
rs7046427	0.85[AFR][1000 genomes]
rs7047062	0.82[AFR][1000 genomes]
rs7049221	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs72760096	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72761903	0.87[AFR][1000 genomes]
rs72761905	0.91[AFR][1000 genomes]
rs72761906	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72761963	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72761964	0.91[AFR][1000 genomes]
rs72761965	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72761966	0.89[AFR][1000 genomes]
rs72761969	0.91[AFR][1000 genomes]
rs72761971	0.91[AFR][1000 genomes]
rs72761973	0.91[AFR][1000 genomes]
rs72761978	0.91[AFR][1000 genomes]
rs72761987	0.89[AFR][1000 genomes]
rs72761992	0.85[AFR][1000 genomes]
rs72761994	0.85[AFR][1000 genomes]
rs72761999	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs72762002	0.85[AFR][1000 genomes]
rs72763803	0.83[AFR][1000 genomes]
rs72763804	0.85[AFR][1000 genomes]
rs72763826	0.82[AFR][1000 genomes]
rs72763828	0.80[AFR][1000 genomes]
rs72763831	0.82[AFR][1000 genomes]
rs72763841	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs72763842	0.82[AFR][1000 genomes]
rs72763846	0.81[AFR][1000 genomes]
rs7848203	0.91[AFR][1000 genomes]
rs7849841	0.91[AFR][1000 genomes]
rs7851718	0.85[AFR][1000 genomes]
rs7851937	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7852118	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7853373	0.85[AFR][1000 genomes]
rs7853792	0.86[AFR][1000 genomes]
rs7854197	0.85[AFR][1000 genomes]
rs7854524	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7855325	0.85[AFR][1000 genomes]
rs7855434	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7856689	0.93[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7857217	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7857943	0.82[AFR][1000 genomes]
rs7860673	0.91[AFR][1000 genomes]
rs7861248	0.91[AFR][1000 genomes]
rs7863159	0.82[AFR][1000 genomes]
rs7864467	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7864645	0.91[AFR][1000 genomes]
rs7864816	0.94[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7867203	0.81[AFR][1000 genomes]
rs7867353	0.86[AFR][1000 genomes]
rs7867430	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7870142	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7870227	0.85[AFR][1000 genomes]
rs7870265	0.90[AFR][1000 genomes]
rs7870912	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7871186	0.82[AFR][1000 genomes]
rs7872283	0.91[AFR][1000 genomes]
rs883025	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs884898	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs884899	0.81[AFR][1000 genomes]
rs9299215	0.91[AFR][1000 genomes]
rs944345	0.83[AFR][1000 genomes]
rs944346	0.83[AFR][1000 genomes]
rs9657641	0.82[AFR][1000 genomes]
rs9657659	0.82[AFR][1000 genomes]
rs9785299	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
2	nsv893747	chr9:116214058-116386438	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv466508	chr9:116244982-116362738	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv615215	chr9:116244982-116362738	Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv526579	chr9:116244982-116391162	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116251600-116283800	Weak transcription	Hela-S3	cervix
2	chr9:116255600-116275800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr9:116264000-116291200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr9:116264800-116298400	Weak transcription	Brain Germinal Matrix	brain
5	chr9:116266800-116281600	Strong transcription	Fetal Stomach	stomach
6	chr9:116268000-116275000	Genic enhancers	HUVEC	blood vessel
7	chr9:116268400-116277200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr9:116268600-116278600	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr9:116269000-116288600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr9:116269400-116288200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr9:116269400-116303000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr9:116269600-116276600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr9:116269600-116298400	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr9:116269800-116276400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr9:116270000-116275000	Enhancers	Stomach Mucosa	stomach
16	chr9:116270400-116289200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr9:116270400-116290600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr9:116270600-116283800	Weak transcription	Colon Smooth Muscle	Colon
19	chr9:116270600-116283800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr9:116270800-116276000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr9:116270800-116276000	Weak transcription	Fetal Brain Female	brain
22	chr9:116270800-116285200	Weak transcription	Brain Substantia Nigra	brain
23	chr9:116270800-116285800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr9:116271000-116285200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr9:116271000-116285600	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr9:116271200-116275000	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr9:116271200-116275000	Enhancers	Spleen	Spleen
28	chr9:116271200-116278200	Weak transcription	Adipose Nuclei	Adipose
29	chr9:116271400-116276000	Weak transcription	Gastric	stomach
30	chr9:116271400-116281200	Weak transcription	Fetal Kidney	kidney
31	chr9:116272000-116276400	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr9:116272000-116278200	Weak transcription	Fetal Lung	lung
33	chr9:116273000-116275200	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr9:116273200-116275000	Enhancers	Placenta	Placenta
35	chr9:116273200-116276600	Enhancers	Fetal Thymus	thymus
36	chr9:116273200-116279400	Genic enhancers	Fetal Intestine Small	intestine
37	chr9:116273200-116279600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr9:116273400-116275200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr9:116273400-116275200	Enhancers	HSMM	muscle
40	chr9:116273400-116279400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr9:116273600-116275000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr9:116273600-116275000	Enhancers	Duodenum Mucosa	Duodenum
43	chr9:116273600-116275600	Weak transcription	Fetal Muscle Trunk	muscle
44	chr9:116273600-116276000	Weak transcription	Aorta	Aorta
45	chr9:116273600-116280400	Strong transcription	Stomach Smooth Muscle	stomach
46	chr9:116273600-116280600	Weak transcription	Brain Hippocampus Middle	brain
47	chr9:116273600-116281400	Weak transcription	Rectal Smooth Muscle	rectum
48	chr9:116273600-116281400	Weak transcription	Right Atrium	heart
49	chr9:116273600-116285400	Weak transcription	Brain Anterior Caudate	brain
50	chr9:116273600-116287000	Weak transcription	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links