Variant report

Variant	rs6438531
Chromosome Location	chr3:119188895-119188896
allele	C/G
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	RELA	chr3:119187241-119189009	GM18505	blood:	n/a	chr3:119188188-119188197 chr3:119188188-119188197
2	MXI1	chr3:119187178-119189165	IMR90	lung:	n/a	n/a
3	NFIC	chr3:119186936-119189087	GM12878	blood:	n/a	n/a
4	MTA3	chr3:119187056-119189103	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:119186977-119189059	GM12891	blood:	n/a	n/a
6	NFIC	chr3:119188248-119189008	GM12878	blood:	n/a	n/a
7	PML	chr3:119186824-119188935	GM12878	blood:	n/a	n/a
8	STAT3	chr3:119188426-119188953	GM12878	blood:	n/a	chr3:119188523-119188531 chr3:119188520-119188528
9	ATF2	chr3:119186893-119189101	GM12878	blood:	n/a	n/a
10	ZNF143	chr3:119188891-119189135	GM12878	blood:	n/a	n/a
11	RUNX3	chr3:119187270-119189209	GM12878	blood:	n/a	n/a
12	MXI1	chr3:119186842-119189206	SK-N-SH	brain:	n/a	n/a
13	RUNX3	chr3:119187354-119189134	GM12878	blood:	n/a	n/a
14	POLR2A	chr3:119186978-119189172	GM12878	blood:	n/a	n/a
15	EBF1	chr3:119188015-119189097	GM12878	blood:	n/a	n/a
16	POLR2A	chr3:119188895-119189047	HepG2	liver:	n/a	n/a
17	POLR2A	chr3:119188673-119188950	HUVEC	blood vessel:	n/a	n/a
18	BCLAF1	chr3:119187411-119189055	GM12878	blood:	n/a	chr3:119188384-119188393 chr3:119187699-119187708 chr3:119188188-119188197
19	RELA	chr3:119187184-119188978	GM12878	blood:	n/a	chr3:119188188-119188197 chr3:119188188-119188197
20	RELA	chr3:119187343-119189019	GM12891	blood:	n/a	chr3:119188188-119188197 chr3:119188188-119188197
21	POLR2A	chr3:119187049-119188976	GM12878	blood:	n/a	n/a
22	WRNIP1	chr3:119188881-119189085	GM12878	blood:	n/a	n/a
23	RELA	chr3:119187451-119188996	GM18951	blood:	n/a	chr3:119188188-119188197 chr3:119188188-119188197

No.	Distal block	Cell Line	Cell type
1	chr3:119186243..119189555-chr3:119215703..119218960,7	K562	blood:
2	chr3:119154291..119156194-chr3:119187536..119190301,2	MCF-7	breast:
3	chr3:119185648..119192167-chr3:119194088..119200916,11	MCF-7	breast:
4	chr3:119180899..119185941-chr3:119186195..119190279,17	K562	blood:
5	chr3:119185037..119191105-chr3:119214944..119221331,23	MCF-7	breast:
6	chr3:119187027..119189715-chr3:119206255..119208346,3	K562	blood:
7	chr3:119187885..119189873-chr3:119203164..119205155,2	K562	blood:
8	chr3:119185641..119191138-chr3:119214841..119219392,9	MCF-7	breast:
9	chr3:119186169..119189555-chr3:119214375..119219589,12	K562	blood:

Variant related genes	Relation type
TMEM39A	TF binding region
ENSG00000272662	Chromatin interaction
ENSG00000113845	Chromatin interaction
ENSG00000176142	Chromatin interaction
ENSG00000163389	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1060569	0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13080905	0.98[ASN][1000 genomes]
rs1797839	0.86[ASN][1000 genomes]
rs1900742	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1919586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1919590	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1967621	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1976919	0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2030816	0.88[AMR][1000 genomes]
rs2177812	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3732413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3814397	0.86[ASN][1000 genomes]
rs4687855	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687860	0.98[ASN][1000 genomes]
rs4688005	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688008	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4688012	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4688014	0.85[ASN][1000 genomes]
rs6414282	0.96[ASN][1000 genomes]
rs6414283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438528	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6438529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438535	1.00[CHB][hapmap];0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6777535	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6778945	0.88[ASN][1000 genomes]
rs6794822	0.96[ASN][1000 genomes]
rs6796970	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs727905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7430798	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7621259	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7628626	0.84[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7630587	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7642502	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9289129	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9809155	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836326	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9836627	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9850447	0.88[ASN][1000 genomes]
rs9867768	0.89[CHB][hapmap];0.88[ASN][1000 genomes]
rs9873196	0.84[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9874480	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9877854	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829695	chr3:119178890-119367996	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119187000-119189000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:119187000-119189200	Active TSS	Fetal Brain Female	brain
3	chr3:119187200-119189200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr3:119187400-119189000	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr3:119187400-119189000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr3:119187600-119189800	Active TSS	GM12878-XiMat	blood
7	chr3:119188200-119189000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
8	chr3:119188200-119189000	Flanking Active TSS	Primary hematopoietic stem cells	blood
9	chr3:119188200-119189000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
10	chr3:119188200-119189000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
11	chr3:119188200-119189000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
12	chr3:119188200-119189000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
13	chr3:119188200-119189000	Flanking Active TSS	Adipose Nuclei	Adipose
14	chr3:119188200-119189000	Flanking Active TSS	Colon Smooth Muscle	Colon
15	chr3:119188200-119189000	Flanking Active TSS	Fetal Brain Male	brain
16	chr3:119188200-119189000	Flanking Active TSS	Fetal Thymus	thymus
17	chr3:119188200-119189000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
18	chr3:119188200-119189000	Flanking Active TSS	HUVEC	blood vessel
19	chr3:119188400-119189000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:119188400-119189000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:119188400-119189000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr3:119188400-119189000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
23	chr3:119188400-119189000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr3:119188400-119189000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
25	chr3:119188400-119189000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:119188400-119189000	Flanking Active TSS	Brain Angular Gyrus	brain
27	chr3:119188400-119189000	Flanking Active TSS	Brain Anterior Caudate	brain
28	chr3:119188400-119189000	Flanking Active TSS	Brain Cingulate Gyrus	brain
29	chr3:119188400-119189000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
30	chr3:119188400-119189000	Flanking Active TSS	Duodenum Mucosa	Duodenum
31	chr3:119188400-119189000	Flanking Active TSS	Fetal Heart	heart
32	chr3:119188400-119189000	Flanking Active TSS	Rectal Smooth Muscle	rectum
33	chr3:119188400-119189000	Flanking Active TSS	A549	lung
34	chr3:119188400-119189000	Flanking Active TSS	HSMMtube	muscle
35	chr3:119188400-119189200	Flanking Active TSS	Primary T cells from cord blood	blood
36	chr3:119188400-119189200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
37	chr3:119188400-119189200	Enhancers	Spleen	Spleen
38	chr3:119188400-119189200	Flanking Active TSS	Hela-S3	cervix
39	chr3:119188400-119189200	Flanking Active TSS	HMEC	breast
40	chr3:119188400-119189600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
41	chr3:119188400-119189800	Weak transcription	Gastric	stomach
42	chr3:119188400-119216200	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr3:119188400-119216800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr3:119188600-119189000	Enhancers	H9 Cell Line	embryonic stem cell
45	chr3:119188600-119189000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr3:119188600-119189000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:119188600-119189000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr3:119188600-119189000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
49	chr3:119188600-119189000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
50	chr3:119188600-119189000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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