Variant report

Variant	rs59417682
Chromosome Location	chr2:38835469-38835470
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38833505..38836464-chr2:38931124..38932679,2	K562	blood:
2	chr2:38832813..38836255-chr2:38838239..38840067,3	MCF-7	breast:
3	chr2:38816516..38836019-chr2:38963690..38980163,62	K562	blood:

Variant related genes	Relation type
ENSG00000115875	Chromatin interaction
ENSG00000152147	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs56686184	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57899462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58770088	1.00[AMR][1000 genomes]
rs60500692	1.00[AMR][1000 genomes]
rs61141629	1.00[AMR][1000 genomes]
rs72895869	1.00[AMR][1000 genomes]
rs72895872	1.00[AMR][1000 genomes]
rs72897624	1.00[AMR][1000 genomes]
rs72905853	1.00[AMR][1000 genomes]
rs72905893	1.00[AMR][1000 genomes]
rs72905899	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72907921	1.00[AFR][1000 genomes]
rs72907927	1.00[AMR][1000 genomes]
rs72907935	1.00[AMR][1000 genomes]
rs72909837	1.00[AFR][1000 genomes]
rs72909858	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv873881	chr2:38745624-38877636	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv581482	chr2:38799820-38858669	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS 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	17 gene(s)	inside rSNPs	diseases
5	nsv581483	chr2:38799820-38862223	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv581484	chr2:38799820-38874177	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38830800-38838600	Weak transcription	Stomach Mucosa	stomach
2	chr2:38831200-38840400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:38831200-38840600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:38831400-38836000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr2:38831400-38836800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:38831400-38838600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr2:38831400-38838800	Weak transcription	Lung	lung
8	chr2:38831400-38840000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr2:38831400-38840800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr2:38832800-38839400	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr2:38834400-38836200	Enhancers	Dnd41	blood
12	chr2:38834600-38835600	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr2:38834600-38837200	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr2:38834600-38837800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr2:38834600-38838000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:38834600-38838600	Enhancers	HepG2	liver
17	chr2:38834800-38836400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr2:38834800-38836600	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr2:38834800-38836600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr2:38835000-38835800	Enhancers	Primary T cells fromperipheralblood	blood
21	chr2:38835200-38835600	Enhancers	GM12878-XiMat	blood
22	chr2:38835200-38836000	Weak transcription	Thymus	Thymus
23	chr2:38835200-38838400	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr2:38835200-38838400	Weak transcription	Osteobl	bone
25	chr2:38835200-38838600	Weak transcription	HSMM	muscle
26	chr2:38835200-38838600	Weak transcription	K562	blood
27	chr2:38835200-38838800	Weak transcription	HSMMtube	muscle
28	chr2:38835200-38839400	Weak transcription	Primary hematopoietic stem cells	blood
29	chr2:38835200-38840000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr2:38835200-38840000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:38835200-38840000	Weak transcription	NHLF	lung
32	chr2:38835200-38840400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr2:38835200-38843400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr2:38835400-38835800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr2:38835400-38837800	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr2:38835400-38837800	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr2:38835400-38838200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr2:38835400-38842000	Weak transcription	HMEC	breast
39	chr2:38835400-38842200	Weak transcription	NHEK	skin
40	chr2:38835400-38843400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr2:38835400-38862400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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