Variant report

Variant	rs12612140
Chromosome Location	chr2:38882577-38882578
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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	chr2:38881069..38883433-chr2:38890460..38892656,2	K562	blood:
5	chr2:38881075..38882966-chr2:38882998..38885867,3	K562	blood:
6	chr2:38879814..38882586-chr2:38892083..38894543,4	K562	blood:

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

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

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12992482	0.80[ASN][1000 genomes]
rs12998892	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13010091	0.80[ASN][1000 genomes]
rs13011896	0.82[ASN][1000 genomes]
rs13015860	0.80[ASN][1000 genomes]
rs13016108	0.80[ASN][1000 genomes]
rs13393767	0.91[EUR][1000 genomes]
rs17022983	0.80[ASN][1000 genomes]
rs17493692	0.80[ASN][1000 genomes]
rs2163553	0.81[EUR][1000 genomes]
rs2163554	0.84[EUR][1000 genomes]
rs2373422	0.80[ASN][1000 genomes]
rs34688430	0.92[AFR][1000 genomes]
rs55948796	0.92[AFR][1000 genomes]
rs6704829	0.89[AFR][1000 genomes]
rs6731029	0.87[AFR][1000 genomes]
rs67326552	0.80[ASN][1000 genomes]
rs6757158	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs891706	0.90[EUR][1000 genomes]

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	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	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
7	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:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38878200-38888400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr2:38878600-38883000	Enhancers	Primary T cells fromperipheralblood	blood
3	chr2:38879000-38882800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr2:38879200-38882800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr2:38879400-38883000	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr2:38879400-38883000	Enhancers	Fetal Thymus	thymus
7	chr2:38880000-38882600	Enhancers	Fetal Intestine Large	intestine
8	chr2:38881000-38882800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr2:38881800-38882800	Enhancers	K562	blood
10	chr2:38881800-38885800	Weak transcription	GM12878-XiMat	blood
11	chr2:38882000-38882800	Enhancers	Thymus	Thymus
12	chr2:38882000-38882800	Enhancers	HepG2	liver
13	chr2:38882000-38884000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr2:38882000-38887600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr2:38882200-38883000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr2:38882200-38886000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr2:38882200-38889800	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr2:38882200-38892800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr2:38882400-38885600	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr2:38882400-38885600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr2:38882400-38887600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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