Variant report

Variant	rs3136242
Chromosome Location	chr2:48012520-48012521
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:48008730..48016091-chr2:48023378..48031018,13	K562	blood:
2	chr2:48011141..48015679-chr2:48023292..48025475,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235369	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10490303	1.00[AMR][1000 genomes]
rs10495948	1.00[AMR][1000 genomes]
rs17036952	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17036971	0.91[AMR][1000 genomes]
rs17037021	0.91[AMR][1000 genomes]
rs17037040	0.90[AMR][1000 genomes]
rs17037062	1.00[AMR][1000 genomes]
rs2134055	0.91[AMR][1000 genomes]
rs2881863	1.00[AMR][1000 genomes]
rs3136274	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3136286	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4381823	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56682209	1.00[AMR][1000 genomes]
rs56881113	0.91[AMR][1000 genomes]
rs58057481	1.00[AMR][1000 genomes]
rs58552166	0.90[AMR][1000 genomes]
rs59624704	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs60118201	1.00[AMR][1000 genomes]
rs60303023	1.00[AMR][1000 genomes]
rs72876814	0.81[EUR][1000 genomes]
rs7560678	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]

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	nsv873999	chr2:47916074-48019485	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	esv3392564	chr2:48009598-48012596	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48009200-48012600	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr2:48009200-48012800	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr2:48009200-48012800	Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr2:48009400-48012600	Active TSS	HSMM	muscle
5	chr2:48009400-48012800	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr2:48009400-48013400	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr2:48009400-48013400	Active TSS	Ovary	ovary
8	chr2:48010000-48013400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr2:48011400-48015000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr2:48011600-48012600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
11	chr2:48011600-48013400	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr2:48011600-48013400	Enhancers	Fetal Brain Male	brain
13	chr2:48011600-48014200	Enhancers	Primary B cells from peripheral blood	blood
14	chr2:48011600-48014200	Transcr. at gene 5' and 3'	Dnd41	blood
15	chr2:48011800-48012600	Enhancers	Lung	lung
16	chr2:48011800-48012600	Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr2:48011800-48013000	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr2:48011800-48013000	Enhancers	Brain Substantia Nigra	brain
19	chr2:48011800-48013000	Enhancers	K562	blood
20	chr2:48011800-48013400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr2:48011800-48013400	Enhancers	Pancreas	Pancrea
22	chr2:48011800-48013600	Enhancers	Primary B cells from cord blood	blood
23	chr2:48011800-48014400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr2:48011800-48023000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr2:48011800-48026200	Weak transcription	Stomach Mucosa	stomach
26	chr2:48012000-48012600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:48012000-48012600	Weak transcription	Brain Angular Gyrus	brain
28	chr2:48012000-48012600	Genic enhancers	Fetal Muscle Trunk	muscle
29	chr2:48012000-48012800	Enhancers	Primary hematopoietic stem cells	blood
30	chr2:48012000-48012800	Enhancers	Liver	Liver
31	chr2:48012000-48012800	Enhancers	Placenta	Placenta
32	chr2:48012000-48012800	Enhancers	Monocytes-CD14+_RO01746	blood
33	chr2:48012000-48013000	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr2:48012000-48013000	Weak transcription	Primary T cells from cord blood	blood
35	chr2:48012000-48013000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr2:48012000-48013000	Weak transcription	Adipose Nuclei	Adipose
37	chr2:48012000-48013000	Enhancers	Brain Cingulate Gyrus	brain
38	chr2:48012000-48013000	Weak transcription	Fetal Lung	lung
39	chr2:48012000-48013000	Weak transcription	NHDF-Ad	bronchial
40	chr2:48012000-48013400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr2:48012000-48013400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr2:48012000-48013400	Enhancers	Colon Smooth Muscle	Colon
43	chr2:48012000-48013400	Enhancers	Duodenum Mucosa	Duodenum
44	chr2:48012000-48013400	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr2:48012000-48013400	Enhancers	Fetal Heart	heart
46	chr2:48012000-48014000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr2:48012000-48014400	Enhancers	Primary T helper cells fromperipheralblood	blood
48	chr2:48012000-48014400	Genic enhancers	Fetal Thymus	thymus
49	chr2:48012000-48015000	Enhancers	Primary T cells fromperipheralblood	blood
50	chr2:48012000-48015200	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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