Variant report

Variant	rs2877453
Chromosome Location	chr8:99055222-99055223
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:24)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:24 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr8:99054791-99055362	HepG2	liver:	n/a	n/a
2	POLR2A	chr8:99055114-99055304	GM12891	blood:	n/a	n/a
3	POLR2A	chr8:99054706-99055256	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr8:99054646-99059519	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr8:99054066-99055341	U87	brain:	n/a	n/a
6	POLR2A	chr8:99054198-99058553	PFSK-1	brain:	n/a	n/a
7	POLR2A	chr8:99055172-99055278	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr8:99054010-99056007	K562	blood:	n/a	n/a
9	POLR2A	chr8:99055151-99055401	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr8:99054530-99058884	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr8:99054790-99055269	GM12891	blood:	n/a	n/a
12	POLR2A	chr8:99055111-99055332	MCF-7	breast:	n/a	n/a
13	POLR2A	chr8:99054857-99055392	HepG2	liver:	n/a	n/a
14	POLR2A	chr8:99050206-99056102	K562	blood:	n/a	n/a
15	POLR2A	chr8:99055170-99055571	K562	blood:	n/a	n/a
16	POLR2A	chr8:99054785-99055657	HepG2	liver:	n/a	n/a
17	POLR2A	chr8:99051437-99058581	PFSK-1	brain:	n/a	n/a
18	POLR2A	chr8:99054840-99055465	A549	lung:	n/a	n/a
19	POLR2A	chr8:99054973-99055448	GM12892	blood:	n/a	n/a
20	POLR2A	chr8:99054736-99058558	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr8:99050185-99058947	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr8:99054635-99055529	PANC-1	pancreas:	n/a	n/a
23	POLR2A	chr8:99050842-99055413	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr8:99054066-99055328	U87	brain:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:99054883..99058427-chr8:99128521..99131598,4	K562	blood:
2	chr8:99054385..99060040-chr8:99125093..99131908,20	MCF-7	breast:
3	chr8:98961024..98963389-chr8:99054505..99057436,2	MCF-7	breast:
4	chr8:98880240..98884584-chr8:99054888..99058750,6	MCF-7	breast:
5	chr8:99055062..99058733-chr8:99305548..99307498,3	MCF-7	breast:
6	chr8:99054555..99060747-chr8:99127722..99132697,23	MCF-7	breast:
7	chr8:99039036..99041305-chr8:99052525..99056666,3	K562	blood:
8	chr8:99054937..99059484-chr8:99117612..99122860,5	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MATN2-1	chr8:99053954-99055555	ENSG00000245970.2
2	lnc-RPL30-3	chr8:99055059-99055435	NONHSAT127901
3	lnc-RPL30-3	chr8:99054873-99055313	NONHSAT127897

No data

Variant related genes	Relation type
SNORA72	TF binding region
ENSG00000104356	Chromatin interaction
ENSG00000104361	Chromatin interaction
ENSG00000132541	Chromatin interaction
ENSG00000132561	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10955147	0.81[AFR][1000 genomes]
rs11775531	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.93[MKK][hapmap];0.88[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11777189	0.91[AFR][1000 genomes]
rs11779647	0.83[MEX][hapmap]
rs11998201	0.80[EUR][1000 genomes]
rs13255477	0.87[ASW][hapmap];0.81[LWK][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs13262105	0.85[AMR][1000 genomes]
rs55698139	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs56137923	0.91[AFR][1000 genomes]
rs6987112	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs7006113	0.82[CEU][hapmap];0.88[MEX][hapmap]
rs7835905	0.81[CEU][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs812	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032904	chr8:98756076-99476925	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv539687	chr8:98756076-99476925	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2877453	RGS22	cis	cerebellum	SCAN
rs2877453	LAPTM4B	cis	lymphoblastoid	seeQTL
rs2877453	DPY19L4	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:99024200-99056000	Weak transcription	Spleen	Spleen
2	chr8:99030600-99056800	Weak transcription	Aorta	Aorta
3	chr8:99031000-99055400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr8:99033800-99055600	Weak transcription	Left Ventricle	heart
5	chr8:99037600-99056400	Weak transcription	Lung	lung
6	chr8:99043600-99055400	Weak transcription	Esophagus	oesophagus
7	chr8:99044800-99057000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr8:99045600-99056800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr8:99046200-99056400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr8:99046400-99055600	Weak transcription	HSMMtube	muscle
11	chr8:99047000-99055800	Weak transcription	Ovary	ovary
12	chr8:99047000-99056400	Weak transcription	Colonic Mucosa	Colon
13	chr8:99050000-99055400	Strong transcription	Fetal Muscle Trunk	muscle
14	chr8:99051000-99055400	Strong transcription	Fetal Thymus	thymus
15	chr8:99051000-99055800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr8:99051800-99055800	Strong transcription	Fetal Intestine Large	intestine
17	chr8:99052000-99055400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr8:99052400-99055400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr8:99052400-99055800	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr8:99052600-99055600	Strong transcription	Placenta	Placenta
21	chr8:99052800-99055600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr8:99052800-99055800	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr8:99053000-99055800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr8:99053400-99055600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr8:99053400-99056000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr8:99053600-99056000	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr8:99053800-99055600	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr8:99053800-99055800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
29	chr8:99054000-99055400	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr8:99054000-99055400	Weak transcription	Pancreas	Pancrea
31	chr8:99054000-99056000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr8:99054200-99055800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr8:99054400-99055400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr8:99054400-99055600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr8:99054400-99055800	Genic enhancers	Primary T cells from cord blood	blood
36	chr8:99054400-99055800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
37	chr8:99054400-99056000	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr8:99054400-99056200	Genic enhancers	Brain Germinal Matrix	brain
39	chr8:99054400-99057400	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
40	chr8:99054400-99057400	Transcr. at gene 5' and 3'	A549	lung
41	chr8:99054600-99055400	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr8:99054600-99055800	Genic enhancers	Fetal Brain Female	brain
43	chr8:99054600-99056000	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr8:99054600-99057200	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
45	chr8:99054600-99057200	Transcr. at gene 5' and 3'	K562	blood
46	chr8:99054600-99057200	Transcr. at gene 5' and 3'	NHEK	skin
47	chr8:99054800-99055400	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
48	chr8:99054800-99055400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr8:99054800-99055400	Genic enhancers	Brain Inferior Temporal Lobe	brain
50	chr8:99054800-99055400	Transcr. at gene 5' and 3'	Duodenum Smooth Muscle	Duodenum

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