Variant report

Variant	rs2987533
Chromosome Location	chr13:49560514-49560515
allele	A/G
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	ZNF384	chr13:49560475-49560532	GM12878	blood:	n/a	n/a
2	ZNF384	chr13:49560419-49560656	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:49510679..49513624-chr13:49558330..49560973,2	K562	blood:

Variant related genes	Relation type
RNU6-60P	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1928109	0.86[JPT][hapmap]
rs1937181	0.86[JPT][hapmap]
rs2987528	0.86[JPT][hapmap]
rs2987530	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]
rs60569686	0.84[AMR][1000 genomes]
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]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv1034	chr13:49526761-49572727	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	nsv900067	chr13:49552271-49594818	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv900068	chr13:49559790-49605774	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2987533	HTR2A	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49551400-49638800	Weak transcription	Pancreas	Pancrea
2	chr13:49551800-49569400	Weak transcription	Psoas Muscle	Psoas
3	chr13:49552200-49570400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr13:49553400-49564800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr13:49553600-49562400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr13:49553600-49596200	Weak transcription	Ovary	ovary
7	chr13:49554000-49565200	Weak transcription	Osteobl	bone
8	chr13:49554200-49564600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr13:49554200-49565400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr13:49554200-49573000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr13:49554200-49573200	Weak transcription	NHDF-Ad	bronchial
12	chr13:49554400-49567400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr13:49554400-49568600	Weak transcription	Placenta	Placenta
14	chr13:49554600-49564600	Weak transcription	Fetal Intestine Small	intestine
15	chr13:49554600-49565600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr13:49554600-49568600	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr13:49555000-49562000	Weak transcription	Primary hematopoietic stem cells	blood
18	chr13:49555000-49564200	Weak transcription	Primary T cells from cord blood	blood
19	chr13:49555000-49569200	Weak transcription	HMEC	breast
20	chr13:49555000-49573000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr13:49555000-49581600	Weak transcription	Left Ventricle	heart
22	chr13:49555200-49563200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr13:49555200-49564800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr13:49555400-49563400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr13:49555600-49564800	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr13:49555800-49563000	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr13:49557000-49561600	Weak transcription	Hela-S3	cervix
28	chr13:49557000-49579800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr13:49557000-49626800	Weak transcription	Right Ventricle	heart
30	chr13:49557200-49563200	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr13:49557200-49573200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr13:49557800-49561800	Weak transcription	Brain Anterior Caudate	brain
33	chr13:49557800-49563400	Weak transcription	Liver	Liver
34	chr13:49557800-49567000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr13:49558000-49563200	Weak transcription	Fetal Heart	heart
36	chr13:49558000-49565200	Weak transcription	Stomach Mucosa	stomach
37	chr13:49558200-49564800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr13:49559800-49560600	Enhancers	Monocytes-CD14+_RO01746	blood
39	chr13:49560000-49561400	ZNF genes & repeats	GM12878-XiMat	blood
40	chr13:49560000-49587600	Weak transcription	Fetal Kidney	kidney
41	chr13:49560200-49560600	Weak transcription	Small Intestine	intestine
42	chr13:49560200-49561400	Weak transcription	Primary B cells from cord blood	blood
43	chr13:49560200-49564800	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr13:49560200-49572000	Weak transcription	Colon Smooth Muscle	Colon
45	chr13:49560200-49578000	Weak transcription	Rectal Smooth Muscle	rectum
46	chr13:49560200-49581000	Weak transcription	Rectal Mucosa Donor 29	rectum

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