Variant report

Variant	rs13011896
Chromosome Location	chr2:38839569-38839570
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38838797..38841106-chr2:38843621..38847033,3	MCF-7	breast:
2	chr2:38838600..38841339-chr2:38925326..38927602,2	K562	blood:
3	chr2:38838640..38841229-chr2:38869315..38872620,3	K562	blood:
4	chr2:38839551..38842960-chr2:38892269..38895636,5	K562	blood:
5	chr2:38830091..38832083-chr2:38838036..38840443,2	MCF-7	breast:
6	chr2:38832813..38836255-chr2:38838239..38840067,3	MCF-7	breast:
7	chr2:38837653..38839575-chr2:38845023..38848760,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143889	Chromatin interaction
ENSG00000143891	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10204680	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12612140	0.82[ASN][1000 genomes]
rs12987111	0.86[AFR][1000 genomes]
rs12990659	0.86[AFR][1000 genomes]
rs12992482	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12996029	0.87[AFR][1000 genomes]
rs13010091	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13015860	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13016108	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13016885	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13025153	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13032371	0.81[EUR][1000 genomes]
rs13415823	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17022983	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17022996	0.85[EUR][1000 genomes]
rs17421743	0.91[AFR][1000 genomes]
rs17493573	0.87[AFR][1000 genomes]
rs17493594	0.83[AFR][1000 genomes]
rs17493692	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1864828	0.90[AFR][1000 genomes]
rs1864829	0.91[AFR][1000 genomes]
rs1864830	0.96[AFR][1000 genomes]
rs2099261	0.81[EUR][1000 genomes]
rs2116383	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2116385	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2163551	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2217537	0.82[EUR][1000 genomes]
rs2373420	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2373421	0.85[EUR][1000 genomes]
rs2373422	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34145681	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34450185	0.83[EUR][1000 genomes]
rs34462852	0.86[AFR][1000 genomes]
rs35273515	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35613649	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35679136	0.89[AFR][1000 genomes]
rs35734673	0.83[AFR][1000 genomes]
rs35861429	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4268910	0.85[AFR][1000 genomes]
rs56217714	0.96[AFR][1000 genomes]
rs67326552	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6742843	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6745023	0.96[AFR][1000 genomes]
rs6745646	0.82[EUR][1000 genomes]
rs6749343	0.95[ASN][1000 genomes]
rs72907903	0.86[AFR][1000 genomes]
rs72909831	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7561778	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7583318	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7600802	0.92[EUR][1000 genomes];0.82[ASN][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	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
7	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38831200-38840400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:38831200-38840600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:38831400-38840000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr2:38831400-38840800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:38835200-38840000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:38835200-38840000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:38835200-38840000	Weak transcription	NHLF	lung
8	chr2:38835200-38840400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr2:38835200-38843400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:38835400-38842000	Weak transcription	HMEC	breast
11	chr2:38835400-38842200	Weak transcription	NHEK	skin
12	chr2:38835400-38843400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr2:38835400-38862400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr2:38837800-38839800	Enhancers	Monocytes-CD14+_RO01746	blood
15	chr2:38837800-38842400	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr2:38838200-38840200	Enhancers	Primary T cells fromperipheralblood	blood
17	chr2:38838600-38840600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr2:38838600-38840600	Enhancers	K562	blood
19	chr2:38838600-38842200	Enhancers	Stomach Mucosa	stomach
20	chr2:38838600-38845000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr2:38838800-38840000	Weak transcription	Duodenum Mucosa	Duodenum
22	chr2:38839000-38839800	Weak transcription	Lung	lung
23	chr2:38839000-38839800	Weak transcription	HSMMtube	muscle
24	chr2:38839000-38839800	Weak transcription	Osteobl	bone
25	chr2:38839000-38840000	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr2:38839000-38840200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr2:38839000-38842000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr2:38839000-38847200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr2:38839200-38839600	Weak transcription	HSMM	muscle
30	chr2:38839200-38839800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr2:38839200-38840200	Enhancers	GM12878-XiMat	blood
32	chr2:38839200-38841800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr2:38839200-38842600	Enhancers	HepG2	liver
34	chr2:38839400-38839800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr2:38839400-38841200	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr2:38839400-38842200	Enhancers	Primary hematopoietic stem cells	blood

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