Variant report

Variant	rs13387435
Chromosome Location	chr2:113391948-113391949
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:113390360..113393063-chr2:113482708..113485504,2	K562	blood:
2	chr2:113390812..113393784-chr2:113396279..113398032,2	MCF-7	breast:
3	chr2:113382212..113385648-chr2:113390770..113393800,3	MCF-7	breast:
4	chr2:113391397..113393329-chr2:113501977..113503565,2	K562	blood:
5	chr2:113389533..113392236-chr2:113492953..113495168,2	K562	blood:
6	chr2:113391817..113395681-chr2:113402206..113404439,3	MCF-7	breast:
7	chr2:113388214..113390218-chr2:113391409..113393753,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144130	Chromatin interaction
ENSG00000237753	Chromatin interaction
ENSG00000144136	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10171024	0.83[EUR][1000 genomes]
rs11680446	0.89[CHB][hapmap]
rs12479380	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs13023016	0.80[CHB][hapmap]
rs4368335	0.94[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs4849084	0.80[CHB][hapmap]
rs4849086	0.83[CEU][hapmap];0.80[CHB][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs908545	0.90[CHB][hapmap];0.85[JPT][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	nsv458997	chr2:113313794-113431092	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats 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	73 gene(s)	inside rSNPs	diseases
2	nsv582708	chr2:113313794-113431092	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv470480	chr2:113373950-113429752	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv428724	chr2:113376894-113555421	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13387435	LRRC49	trans	cerebellum	SCAN
rs13387435	IL1F10	cis	parietal	SCAN
rs13387435	IL3	trans	cerebellum	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113384200-113392400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:113385000-113396000	Weak transcription	Colonic Mucosa	Colon
3	chr2:113385000-113402600	Weak transcription	Esophagus	oesophagus
4	chr2:113385800-113401800	Weak transcription	Brain Hippocampus Middle	brain
5	chr2:113388800-113394800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr2:113388800-113398200	Weak transcription	Lung	lung
7	chr2:113389000-113395000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr2:113389000-113395000	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr2:113389200-113394800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr2:113389200-113394800	Enhancers	Fetal Thymus	thymus
11	chr2:113389400-113395000	Enhancers	Primary T cells fromperipheralblood	blood
12	chr2:113389400-113402000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr2:113389600-113392000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr2:113389600-113393800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr2:113389600-113394000	Weak transcription	Spleen	Spleen
16	chr2:113389600-113394800	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr2:113389600-113395000	Enhancers	Primary T cells from cord blood	blood
18	chr2:113389600-113402200	Weak transcription	Primary B cells from cord blood	blood
19	chr2:113389800-113392600	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr2:113389800-113392600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr2:113389800-113393600	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr2:113389800-113393800	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr2:113389800-113393800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr2:113389800-113394000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr2:113389800-113395200	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr2:113389800-113398400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr2:113389800-113400400	Weak transcription	Fetal Intestine Small	intestine
28	chr2:113390000-113394000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:113390000-113396800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:113390000-113397200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:113390000-113398000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr2:113390600-113392000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr2:113390600-113393400	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr2:113390600-113394600	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr2:113390800-113397400	Weak transcription	K562	blood
36	chr2:113391200-113392200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr2:113391200-113392600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr2:113391200-113392600	Enhancers	Placenta Amnion	Placenta Amnion
39	chr2:113391200-113393000	Enhancers	Placenta	Placenta
40	chr2:113391400-113392000	Enhancers	HMEC	breast
41	chr2:113391400-113392200	Flanking Bivalent TSS/Enh	HepG2	liver
42	chr2:113391400-113394000	Enhancers	GM12878-XiMat	blood
43	chr2:113391400-113394800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr2:113391400-113398000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr2:113391600-113392800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr2:113391800-113392000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
47	chr2:113391800-113392200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr2:113391800-113393200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
49	chr2:113391800-113395000	Enhancers	Primary T killer memory cells from peripheral blood	blood

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