Variant report

Variant	rs6744400
Chromosome Location	chr2:38890705-38890706
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38890666..38892556-chr2:38947054..38950004,2	K562	blood:
2	chr2:38888499..38891196-chr2:38892046..38897483,5	K562	blood:
3	chr2:38828302..38829916-chr2:38889127..38891080,2	K562	blood:
4	chr2:38881069..38883433-chr2:38890460..38892656,2	K562	blood:

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

Extended variants
information (count: 24 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11688977	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11689051	0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12712609	0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs13387464	0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs28551538	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3821023	0.98[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4670262	0.86[EUR][1000 genomes]
rs4670263	0.96[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4670882	0.86[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4670883	0.93[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6732137	0.96[ASN][1000 genomes]
rs6761563	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7571326	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7574493	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7588762	0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7590750	0.98[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7590835	0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7590926	0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7597535	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][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	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	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:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38882200-38892800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr2:38882800-38891200	Weak transcription	K562	blood
3	chr2:38882800-38892800	Weak transcription	Thymus	Thymus
4	chr2:38886600-38892200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr2:38887600-38892600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr2:38888400-38892800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr2:38888800-38890800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:38888800-38891000	Weak transcription	Osteobl	bone
9	chr2:38888800-38891200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr2:38888800-38892800	Weak transcription	HSMMtube	muscle
11	chr2:38889000-38890800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:38889600-38891200	Enhancers	Primary T cells fromperipheralblood	blood
13	chr2:38889800-38891800	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr2:38889800-38892800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr2:38889800-38892800	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr2:38890200-38892200	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr2:38890200-38892800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr2:38890200-38892800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr2:38890400-38891000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr2:38890400-38892200	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr2:38890400-38892400	Weak transcription	Duodenum Mucosa	Duodenum
22	chr2:38890600-38891000	Enhancers	GM12878-XiMat	blood
23	chr2:38890600-38891400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr2:38890600-38892600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr2:38890600-38892800	Weak transcription	Monocytes-CD14+_RO01746	blood

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