Variant report

Variant	rs2987530
Chromosome Location	chr13:49607414-49607415
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:49604135..49605802-chr13:49605947..49607714,2	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1928109	0.86[JPT][hapmap]
rs1937181	0.86[JPT][hapmap]
rs2987528	0.86[JPT][hapmap]
rs2987533	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2994377	0.86[JPT][hapmap]
rs2994378	0.86[JPT][hapmap]
rs2994379	0.86[JPT][hapmap]
rs2994380	0.86[JPT][hapmap]
rs3012116	0.86[JPT][hapmap]
rs3012117	0.86[JPT][hapmap]
rs3012121	0.86[JPT][hapmap]
rs3012127	0.91[JPT][hapmap]
rs3012133	0.86[JPT][hapmap]
rs3012136	0.86[JPT][hapmap]
rs736222	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7998359	0.88[JPT][hapmap]
rs9535126	0.86[JPT][hapmap]
rs9535145	0.86[JPT][hapmap]
rs9535154	0.82[JPT][hapmap]
rs9535155	0.82[JPT][hapmap]
rs9535166	0.82[JPT][hapmap]
rs9535167	0.82[JPT][hapmap]

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	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv455882	chr13:49531551-49679157	Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv561593	chr13:49531551-49679157	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats 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	17 gene(s)	inside rSNPs	diseases
4	esv1793883	chr13:49543723-49789164	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS 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	20 gene(s)	inside rSNPs	diseases
5	esv1803100	chr13:49576474-49655941	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2987530	HTR2A	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49551400-49638800	Weak transcription	Pancreas	Pancrea
2	chr13:49557000-49626800	Weak transcription	Right Ventricle	heart
3	chr13:49568800-49626800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr13:49568800-49627000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr13:49573400-49634800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr13:49582200-49659000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr13:49582800-49617600	Weak transcription	Liver	Liver
8	chr13:49584000-49616600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr13:49584200-49649200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr13:49584600-49613800	Weak transcription	Left Ventricle	heart
11	chr13:49584800-49612400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr13:49587800-49611400	Weak transcription	Fetal Kidney	kidney
13	chr13:49587800-49626600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr13:49592800-49649600	Weak transcription	Fetal Intestine Large	intestine
15	chr13:49593400-49611800	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr13:49594800-49636000	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr13:49596400-49611600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr13:49596400-49626800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr13:49596800-49609200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr13:49597200-49619600	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr13:49597200-49626600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr13:49598000-49650200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr13:49598600-49626800	Weak transcription	Osteobl	bone
24	chr13:49598800-49617600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr13:49599000-49614200	Weak transcription	Hela-S3	cervix
26	chr13:49599000-49649200	Weak transcription	Primary B cells from peripheral blood	blood
27	chr13:49601000-49616200	Weak transcription	Fetal Lung	lung
28	chr13:49601400-49620400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr13:49601600-49620000	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr13:49601600-49623800	Weak transcription	Fetal Stomach	stomach
31	chr13:49601800-49660600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr13:49603200-49649200	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr13:49603200-49652200	Weak transcription	Dnd41	blood
34	chr13:49603400-49613400	Weak transcription	Placenta	Placenta
35	chr13:49603400-49623800	Weak transcription	Fetal Intestine Small	intestine
36	chr13:49604200-49611600	Weak transcription	Primary T cells from cord blood	blood
37	chr13:49604600-49610400	Weak transcription	Primary hematopoietic stem cells	blood
38	chr13:49604600-49625200	Weak transcription	Primary B cells from cord blood	blood
39	chr13:49604600-49626800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr13:49604800-49611600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr13:49604800-49618800	Weak transcription	GM12878-XiMat	blood
42	chr13:49604800-49636400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr13:49605200-49643400	Weak transcription	HSMM	muscle
44	chr13:49605600-49613800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr13:49607400-49607600	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet

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