Variant report

Variant	rs10490303
Chromosome Location	chr2:48039484-48039485
allele	A/C
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	POLR2A	chr2:48038699-48040606	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr2:48037613-48040378	GM12891	blood:	n/a	n/a
3	POLR2A	chr2:48038340-48040041	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr2:48038075-48040082	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr2:48038490-48039495	H1-hESC	embryonic stem cell:	n/a	n/a
6	BCL3	chr2:48038512-48040663	A549	lung:	n/a	chr2:48039310-48039319
7	POLR2A	chr2:48038677-48040184	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr2:48038792-48040444	SK-N-MC	brain:	n/a	n/a
9	NFATC1	chr2:48038702-48039593	GM12878	blood:	n/a	n/a
10	POLR2A	chr2:48038749-48039539	GM12878	blood:	n/a	n/a
11	BCL3	chr2:48038714-48040076	A549	lung:	n/a	chr2:48039310-48039319
12	POLR2A	chr2:48037237-48040050	MCF-7	breast:	n/a	n/a
13	POLR2A	chr2:48039458-48039509	K562	blood:	n/a	n/a
14	POLR2A	chr2:48038736-48040461	A549	lung:	n/a	n/a
15	POLR2A	chr2:48038577-48040314	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr2:48039341-48039835	HepG2	liver:	n/a	n/a
17	POLR2A	chr2:48038443-48039672	HL-60	blood:	n/a	n/a
18	POLR2A	chr2:48038818-48039653	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr2:48033015-48040519	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr2:48038715-48039619	HepG2	liver:	n/a	n/a
21	POLR2A	chr2:48038661-48039484	GM12892	blood:	n/a	n/a
22	POLR2A	chr2:48039388-48039548	HUVEC	blood vessel:	n/a	n/a
23	POLR2A	chr2:48039154-48039560	SK-N-SH	brain:	n/a	n/a
24	POLR2A	chr2:48022295-48040595	K562	blood:	n/a	n/a
25	POLR2A	chr2:48038686-48040507	GM12878	blood:	n/a	n/a
26	POLR2A	chr2:48038828-48040002	HepG2	liver:	n/a	n/a
27	GATA3	chr2:48039308-48039764	SH-SY5Y	brain:	n/a	n/a
28	POLR2A	chr2:48038175-48039955	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:48034542..48037222-chr2:48039301..48041278,3	MCF-7	breast:

Variant related genes	Relation type
FBXO11	TF binding region
ENSG00000138081	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10495948	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17036952	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes]
rs17036971	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17037021	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17037040	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17037055	1.00[CEU][hapmap]
rs17037062	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17037064	1.00[CEU][hapmap]
rs2134055	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2881863	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3136242	1.00[AMR][1000 genomes]
rs3136274	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3136286	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4381823	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56682209	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56881113	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs58057481	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58552166	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs59624704	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs60118201	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60303023	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6704872	0.88[GIH][hapmap]
rs72876814	0.93[EUR][1000 genomes]
rs7560678	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998096	chr2:47939614-48131697	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1009769	chr2:47972642-48509765	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv535680	chr2:47972642-48509765	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48012600-48065000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:48016200-48050400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
3	chr2:48017000-48049400	Strong transcription	Fetal Intestine Large	intestine
4	chr2:48017200-48053200	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr2:48017400-48049600	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr2:48021200-48051600	Strong transcription	Placenta	Placenta
7	chr2:48021400-48067600	Strong transcription	Dnd41	blood
8	chr2:48021600-48067000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:48021800-48039800	Strong transcription	Brain Anterior Caudate	brain
10	chr2:48022000-48041400	Strong transcription	HSMM	muscle
11	chr2:48022200-48050200	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr2:48022800-48049200	Strong transcription	Rectal Mucosa Donor 31	rectum
13	chr2:48022800-48050000	Strong transcription	HUVEC	blood vessel
14	chr2:48023200-48065000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr2:48029200-48040200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
16	chr2:48030200-48067600	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr2:48030400-48044200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr2:48030400-48067000	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr2:48030800-48040000	Strong transcription	Brain Germinal Matrix	brain
20	chr2:48030800-48040600	Strong transcription	HMEC	breast
21	chr2:48030800-48041400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr2:48030800-48047200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr2:48030800-48048000	Strong transcription	Hela-S3	cervix
24	chr2:48030800-48049400	Strong transcription	Fetal Muscle Trunk	muscle
25	chr2:48030800-48049600	Strong transcription	Duodenum Mucosa	Duodenum
26	chr2:48030800-48067000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr2:48030800-48067000	Strong transcription	Fetal Thymus	thymus
28	chr2:48031000-48040400	Strong transcription	NH-A	brain
29	chr2:48031000-48042400	Strong transcription	A549	lung
30	chr2:48031000-48049400	Strong transcription	Fetal Brain Female	brain
31	chr2:48031000-48053000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr2:48031000-48067000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr2:48031000-48067000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr2:48031000-48067200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr2:48031200-48048600	Strong transcription	K562	blood
36	chr2:48031200-48049600	Strong transcription	Primary B cells from cord blood	blood
37	chr2:48031200-48053800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:48031200-48065800	Strong transcription	Liver	Liver
39	chr2:48031200-48066800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr2:48031400-48040000	Strong transcription	Primary T cells from cord blood	blood
41	chr2:48031400-48040000	Strong transcription	Primary hematopoietic stem cells	blood
42	chr2:48031400-48042000	Weak transcription	Esophagus	oesophagus
43	chr2:48031400-48042800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr2:48031400-48042800	Weak transcription	Aorta	Aorta
45	chr2:48031400-48046400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr2:48031400-48050000	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr2:48031400-48051400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr2:48031400-48060600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr2:48031400-48066800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr2:48031400-48067000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links