Variant report

Variant	rs559678259
Chromosome Location	chr2:38881539-38881540
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:38827420..38830831-chr2:38879840..38883102,4	K562	blood:
2	chr2:38857535..38860181-chr2:38880883..38883565,2	K562	blood:
3	chr2:38879772..38882593-chr2:38978947..38981476,2	K562	blood:
4	chr2:38827470..38830831-chr2:38880188..38882467,3	K562	blood:
5	chr2:38880141..38882510-chr2:38904571..38906681,2	K562	blood:
6	chr2:38881069..38883433-chr2:38890460..38892656,2	K562	blood:
7	chr2:38881075..38882966-chr2:38882998..38885867,3	K562	blood:
8	chr2:38879814..38882586-chr2:38892083..38894543,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000235586	Chromatin interaction
ENSG00000143889	Chromatin interaction
ENSG00000143891	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	nsv581485	chr2:38839323-38893660	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv873882	chr2:38858669-38921498	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv2762495	chr2:38861095-38886391	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	esv3457549	chr2:38871768-38882574	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	esv3457553	chr2:38871805-38882546	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	esv3457551	chr2:38871805-38882561	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	esv3457550	chr2:38871849-38882546	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	esv14023	chr2:38871950-38882521	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	esv2760617	chr2:38873799-38886391	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
12	nsv873883	chr2:38881106-38932777	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38870800-38881600	Weak transcription	Spleen	Spleen
2	chr2:38876000-38882000	Weak transcription	Thymus	Thymus
3	chr2:38877200-38882000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr2:38877200-38882200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr2:38878200-38888400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr2:38878400-38882000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr2:38878600-38883000	Enhancers	Primary T cells fromperipheralblood	blood
8	chr2:38878800-38881600	Enhancers	Stomach Mucosa	stomach
9	chr2:38879000-38882000	Enhancers	Placenta	Placenta
10	chr2:38879000-38882800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr2:38879200-38882800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr2:38879400-38882200	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr2:38879400-38882200	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr2:38879400-38883000	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr2:38879400-38883000	Enhancers	Fetal Thymus	thymus
16	chr2:38879600-38881600	Enhancers	Hela-S3	cervix
17	chr2:38879600-38882000	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr2:38880000-38882600	Enhancers	Fetal Intestine Large	intestine
19	chr2:38880200-38881800	Enhancers	Fetal Intestine Small	intestine
20	chr2:38880200-38881800	Enhancers	GM12878-XiMat	blood
21	chr2:38880200-38882400	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr2:38880400-38882000	Enhancers	Primary hematopoietic stem cells	blood
23	chr2:38880600-38882000	Flanking Active TSS	HepG2	liver
24	chr2:38880600-38882200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
25	chr2:38880800-38882000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr2:38880800-38882000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr2:38880800-38882200	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr2:38880800-38882400	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr2:38880800-38882400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr2:38881000-38881800	Flanking Active TSS	K562	blood
31	chr2:38881000-38882200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr2:38881000-38882400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr2:38881000-38882800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr2:38881400-38881600	Enhancers	Rectal Mucosa Donor 29	rectum
35	chr2:38881400-38881800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr2:38881400-38882000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links