Variant report

Variant	rs2802243
Chromosome Location	chr13:30081749-30081750
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:30074865..30078261-chr13:30079505..30082420,3	K562	blood:
2	chr13:30080252..30082787-chr13:30168162..30169965,2	MCF-7	breast:
3	chr13:30081296..30083385-chr13:30689063..30690673,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139514	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs12427581	1.00[ASW][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap]
rs12428751	0.82[JPT][hapmap];1.00[MEX][hapmap]
rs17073661	1.00[JPT][hapmap]
rs17073703	0.82[ASW][hapmap]
rs17660515	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2277452	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2482087	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2482089	1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2482090	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2482092	0.90[AFR][1000 genomes]
rs2482097	0.91[CHD][hapmap];0.92[ASN][1000 genomes]
rs2490264	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2490266	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2490267	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2490268	0.84[CHD][hapmap];0.92[ASN][1000 genomes]
rs2776952	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2776953	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2776955	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2776956	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2776958	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2776960	0.93[YRI][hapmap];0.90[AFR][1000 genomes]
rs2776978	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2776979	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2776980	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2776981	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2776983	0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2776984	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2776985	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2776986	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2802240	1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2802244	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2802245	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2802246	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2802250	0.81[CHD][hapmap]
rs2989592	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3011618	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs3011619	0.81[CHD][hapmap];0.87[LWK][hapmap];1.00[MKK][hapmap];0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs3011620	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011622	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011623	1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3011624	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3011625	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3013640	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3013641	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs598281	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv983696	chr13:30034016-30090454	Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv430551	chr13:30061100-30113000	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv899960	chr13:30064014-30097240	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv561392	chr13:30071245-30091819	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2802243	PRELP	trans	brain	seeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30062400-30087200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr13:30066400-30084400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr13:30071000-30128800	Strong transcription	Dnd41	blood
4	chr13:30072800-30082600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr13:30074800-30082600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr13:30074800-30084800	Weak transcription	Gastric	stomach
7	chr13:30077600-30081800	Weak transcription	Fetal Brain Male	brain
8	chr13:30077600-30082000	Weak transcription	Brain Germinal Matrix	brain
9	chr13:30077600-30082000	Weak transcription	Fetal Brain Female	brain
10	chr13:30077600-30082200	Weak transcription	Esophagus	oesophagus
11	chr13:30077800-30085200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr13:30077800-30085600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr13:30077800-30087800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr13:30078000-30082200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr13:30078000-30084800	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr13:30078000-30086000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr13:30078400-30082200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr13:30078400-30082600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr13:30078600-30082000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr13:30078600-30082400	Weak transcription	Right Ventricle	heart
21	chr13:30079000-30085800	Weak transcription	Primary T cells from cord blood	blood
22	chr13:30079200-30082200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr13:30079600-30087200	Weak transcription	HUVEC	blood vessel
24	chr13:30079800-30082000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr13:30079800-30084200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr13:30080000-30084200	Weak transcription	NHEK	skin
27	chr13:30080000-30084400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr13:30080000-30084800	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr13:30080000-30085000	Weak transcription	HMEC	breast
30	chr13:30080000-30085600	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr13:30080000-30087200	Weak transcription	Aorta	Aorta
32	chr13:30080200-30084200	Weak transcription	Thymus	Thymus
33	chr13:30080200-30087200	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr13:30080200-30087800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr13:30080400-30081800	Bivalent Enhancer	Fetal Muscle Leg	muscle
36	chr13:30080400-30083000	Enhancers	Pancreas	Pancrea
37	chr13:30080400-30083200	Enhancers	HSMMtube	muscle
38	chr13:30080400-30085600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr13:30080400-30086600	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr13:30080600-30085000	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr13:30080600-30086600	Weak transcription	Fetal Thymus	thymus
42	chr13:30080600-30088200	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr13:30080800-30082200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
44	chr13:30080800-30082200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
45	chr13:30081000-30081800	Bivalent Enhancer	Fetal Kidney	kidney
46	chr13:30081000-30082200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr13:30081000-30082400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr13:30081000-30082400	Enhancers	Ovary	ovary
49	chr13:30081000-30083400	Enhancers	Left Ventricle	heart
50	chr13:30081000-30084600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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