Variant report

Variant	rs6729679
Chromosome Location	chr2:38890909-38890910
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXM1	chr2:38890889-38891475	GM12878	blood:	n/a	n/a
2	ATF2	chr2:38890859-38891427	GM12878	blood:	n/a	n/a
3	MAX	chr2:38890905-38891310	NB4	blood:	n/a	chr2:38891174-38891183
4	RUNX3	chr2:38890901-38891428	GM12878	blood:	n/a	n/a
5	FOXM1	chr2:38890779-38891519	GM12878	blood:	n/a	n/a
6	POLR2A	chr2:38890884-38891399	SK-N-MC	brain:	n/a	n/a
7	MTA3	chr2:38890861-38891441	GM12878	blood:	n/a	n/a
8	RUNX3	chr2:38890908-38891353	GM12878	blood:	n/a	n/a
9	NFIC	chr2:38890805-38891536	GM12878	blood:	n/a	n/a
10	MXI1	chr2:38890838-38891445	IMR90	lung:	n/a	n/a
11	BCLAF1	chr2:38890899-38891425	GM12878	blood:	n/a	n/a

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
GALM	TF binding region
ENSG00000143889	Chromatin interaction
ENSG00000143891	Chromatin interaction
ENSG00000235586	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12611538	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12611916	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12618339	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6717650	1.00[ASN][1000 genomes]
rs73930831	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73930943	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs752987	1.00[EUR][1000 genomes];1.00[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:27 , 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	chr2:38888800-38891000	Weak transcription	Osteobl	bone
8	chr2:38888800-38891200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:38888800-38892800	Weak transcription	HSMMtube	muscle
10	chr2:38889600-38891200	Enhancers	Primary T cells fromperipheralblood	blood
11	chr2:38889800-38891800	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr2:38889800-38892800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr2:38889800-38892800	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr2:38890200-38892200	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr2:38890200-38892800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr2:38890200-38892800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr2:38890400-38891000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr2:38890400-38892200	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr2:38890400-38892400	Weak transcription	Duodenum Mucosa	Duodenum
20	chr2:38890600-38891000	Enhancers	GM12878-XiMat	blood
21	chr2:38890600-38891400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr2:38890600-38892600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr2:38890600-38892800	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr2:38890800-38891000	Enhancers	Primary B cells from cord blood	blood
25	chr2:38890800-38891000	Enhancers	Primary hematopoietic stem cells	blood
26	chr2:38890800-38892600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:38890800-38892800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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