Variant report

Variant	rs2908550
Chromosome Location	chr7:56167081-56167082
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:40)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:40 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:56165849-56169236	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr7:56166041-56167350	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr7:56166076-56169320	GM12878	blood:	n/a	n/a
4	POLR2A	chr7:56167048-56169396	K562	blood:	n/a	n/a
5	POLR2A	chr7:56167023-56169284	HepG2	liver:	n/a	n/a
6	POLR2A	chr7:56166044-56170051	K562	blood:	n/a	n/a
7	POLR2A	chr7:56166771-56169276	A549	lung:	n/a	n/a
8	POLR2A	chr7:56165178-56175093	K562	blood:	n/a	n/a
9	POLR2A	chr7:56166621-56167323	K562	blood:	n/a	n/a
10	POLR2A	chr7:56166020-56169262	K562	blood:	n/a	n/a
11	POLR2A	chr7:56167059-56169406	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr7:56167072-56167636	PANC-1	pancreas:	n/a	n/a
13	POLR2A	chr7:56166645-56167113	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr7:56166185-56168586	GM12891	blood:	n/a	n/a
15	POLR2A	chr7:56166883-56169354	K562	blood:	n/a	n/a
16	POLR2A	chr7:56166012-56168947	PFSK-1	brain:	n/a	n/a
17	POLR2A	chr7:56167019-56168645	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr7:56166562-56169354	K562	blood:	n/a	n/a
19	POLR2A	chr7:56165333-56169250	GM12878	blood:	n/a	n/a
20	POLR2A	chr7:56167033-56168683	HL-60	blood:	n/a	n/a
21	POLR2A	chr7:56165965-56169413	GM12892	blood:	n/a	n/a
22	POLR2A	chr7:56166941-56168156	PFSK-1	brain:	n/a	n/a
23	POLR2A	chr7:56166059-56169202	K562	blood:	n/a	n/a
24	POLR2A	chr7:56166128-56169485	GM12878	blood:	n/a	n/a
25	POLR2A	chr7:56166001-56169490	K562	blood:	n/a	n/a
26	POLR2A	chr7:56165277-56169953	GM12891	blood:	n/a	n/a
27	POLR2A	chr7:56165910-56168620	GM12892	blood:	n/a	n/a
28	POLR2A	chr7:56166119-56169320	K562	blood:	n/a	n/a
29	POLR2A	chr7:56166032-56169378	GM12878	blood:	n/a	n/a
30	POLR2A	chr7:56165976-56169224	HepG2	liver:	n/a	n/a
31	POLR2A	chr7:56167026-56170027	HepG2	liver:	n/a	n/a
32	POLR2A	chr7:56166827-56169224	HepG2	liver:	n/a	n/a
33	POLR2A	chr7:56165201-56169237	IMR90	lung:	n/a	n/a
34	POLR2A	chr7:56166996-56169232	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr7:56167062-56168247	NB4	blood:	n/a	n/a
36	POLR2A	chr7:56165022-56169038	GM12892	blood:	n/a	n/a
37	POLR2A	chr7:56165939-56169331	GM12892	blood:	n/a	n/a
38	POLR2A	chr7:56166510-56169218	GM12891	blood:	n/a	n/a
39	POLR2A	chr7:56166079-56169024	GM12891	blood:	n/a	n/a
40	POLR2A	chr7:56166955-56167280	Hela-S3	cervix:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:56166954..56169953-chr7:56173700..56175335,2	MCF-7	breast:
2	chr7:56158331..56162402-chr7:56164304..56169225,5	K562	blood:
3	chr7:56165783..56167904-chr7:56180096..56183560,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000238673	TF binding region
ENSG00000106153	Chromatin interaction
ENSG00000164776	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10255049	0.84[ASN][1000 genomes]
rs10258800	0.86[AMR][1000 genomes]
rs11238394	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11773374	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11773453	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12537943	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13234899	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13242830	0.86[AMR][1000 genomes]
rs13244654	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1894832	0.86[AMR][1000 genomes]
rs2002651	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2016482	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2016724	0.83[AMR][1000 genomes]
rs2331180	0.86[AMR][1000 genomes]
rs2538047	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2908543	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2908544	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2908545	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4947536	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4948106	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6945795	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7782243	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7783339	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7793921	0.86[ASN][1000 genomes]
rs7799471	0.86[AMR][1000 genomes]
rs7801169	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs816408	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs816409	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs816411	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs933466	0.86[AMR][1000 genomes]
rs9767946	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829874	chr7:55382925-56369816	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv995105	chr7:55606107-56174888	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	esv12412	chr7:55619800-56385412	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv949574	chr7:55705566-56544711	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	esv3446617	chr7:55745934-56485903	Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
6	nsv529162	chr7:55800753-56174888	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	esv2761334	chr7:55823581-56424739	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
8	nsv1018806	chr7:55844931-56383936	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
9	nsv538860	chr7:55844931-56383936	Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
10	nsv498114	chr7:55872850-56174888	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
11	nsv1034712	chr7:56146885-56605592	Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
12	nsv538861	chr7:56146885-56605592	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56134000-56167800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr7:56134200-56167600	Weak transcription	Small Intestine	intestine
3	chr7:56138800-56167600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr7:56142000-56168000	Weak transcription	GM12878-XiMat	blood
5	chr7:56142200-56167800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr7:56146000-56167800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr7:56147000-56167400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr7:56147400-56169800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr7:56147600-56167200	Weak transcription	HMEC	breast
10	chr7:56147600-56167400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr7:56147800-56167200	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr7:56147800-56167400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr7:56148000-56167200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr7:56148800-56167400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr7:56149600-56167200	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr7:56149800-56167600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr7:56149800-56168000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr7:56152000-56167400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr7:56155600-56167200	Weak transcription	Primary B cells from peripheral blood	blood
20	chr7:56155600-56167400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr7:56155600-56167600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr7:56156800-56167400	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr7:56157800-56167600	Weak transcription	K562	blood
24	chr7:56158200-56173200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr7:56159600-56168200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr7:56160600-56167400	Weak transcription	Aorta	Aorta
27	chr7:56160600-56167600	Weak transcription	Psoas Muscle	Psoas
28	chr7:56160800-56170400	Weak transcription	Fetal Brain Male	brain
29	chr7:56161000-56167200	Weak transcription	HSMMtube	muscle
30	chr7:56161000-56167200	Weak transcription	NHEK	skin
31	chr7:56161000-56167400	Weak transcription	Brain Angular Gyrus	brain
32	chr7:56161000-56167600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr7:56161000-56167600	Weak transcription	HSMM	muscle
34	chr7:56161000-56173000	Weak transcription	Fetal Heart	heart
35	chr7:56161200-56167200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr7:56161200-56167200	Weak transcription	Brain Anterior Caudate	brain
37	chr7:56161200-56167200	Weak transcription	Brain Cingulate Gyrus	brain
38	chr7:56161200-56167200	Weak transcription	Brain Hippocampus Middle	brain
39	chr7:56161200-56167200	Weak transcription	Brain Substantia Nigra	brain
40	chr7:56161200-56167200	Weak transcription	Fetal Lung	lung
41	chr7:56161200-56167200	Weak transcription	Fetal Muscle Trunk	muscle
42	chr7:56161200-56167200	Weak transcription	Placenta	Placenta
43	chr7:56161200-56167200	Weak transcription	NH-A	brain
44	chr7:56161200-56167400	Weak transcription	Brain Germinal Matrix	brain
45	chr7:56161200-56167400	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr7:56161200-56167600	Weak transcription	Colonic Mucosa	Colon
47	chr7:56161200-56167600	Weak transcription	Esophagus	oesophagus
48	chr7:56161200-56167600	Weak transcription	Left Ventricle	heart
49	chr7:56161200-56167600	Weak transcription	Right Ventricle	heart
50	chr7:56161200-56167600	Weak transcription	Spleen	Spleen

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