Variant report

Variant	rs11709461
Chromosome Location	chr3:133380026-133380027
allele	A/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	MXI1	chr3:133380026-133382054	IMR90	lung:	n/a	n/a
2	E2F4	chr3:133379686-133381461	MCF10A-Er-Src	breast:	n/a	chr3:133380784-133380792 chr3:133380785-133380796 chr3:133380785-133380796 chr3:133380785-133380792 chr3:133380785-133380792 chr3:133380683-133380693 chr3:133380783-133380794 chr3:133380785-133380792
3	HCFC1	chr3:133379838-133381572	Hela-S3	cervix:	n/a	n/a
4	SIN3A	chr3:133379938-133381431	H1-hESC	embryonic stem cell:	n/a	chr3:133380580-133380588 chr3:133380697-133380708 chr3:133380661-133380672
5	MXI1	chr3:133380019-133381182	GM12878	blood:	n/a	n/a
6	POLR2A	chr3:133379816-133381451	MCF10A-Er-Src	breast:	n/a	n/a
7	MXI1	chr3:133379290-133381643	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr3:133379978-133381535	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:133378019..133382399-chr3:133522860..133528810,6	K562	blood:
2	chr3:133373411..133375174-chr3:133378330..133380053,2	K562	blood:
3	chr3:133375493..133377434-chr3:133377728..133380427,4	K562	blood:
4	chr3:133371314..133375654-chr3:133378564..133381849,6	K562	blood:
5	chr3:133379614..133382648-chr3:133523517..133526970,4	MCF-7	breast:
6	chr3:133378243..133380409-chr3:133529566..133531279,2	MCF-7	breast:
7	chr19:55918692..55919573-chr3:133379900..133380571,2	Hela-S3	cervix:
8	chr3:133292114..133294655-chr3:133378270..133380553,3	K562	blood:
9	chr3:133374912..133377513-chr3:133379480..133381997,2	MCF-7	breast:

Variant related genes	Relation type
TOPBP1	TF binding region
TFP1	TF binding region
RNU6-678P	TF binding region
ENSG00000108106	Chromatin interaction
ENSG00000144867	Chromatin interaction
ENSG00000163781	Chromatin interaction
ENSG00000091527	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10512903	1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10512904	0.90[CEU][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10512907	0.89[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10512908	0.90[CEU][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10512909	0.84[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11706413	0.90[CEU][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11706586	0.90[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11706809	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11707750	0.90[CEU][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11708197	0.90[CEU][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11708532	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11708565	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11709132	0.89[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11709349	0.90[CEU][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11709404	0.90[CEU][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11709940	0.88[CEU][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11710111	0.84[CEU][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11711706	0.88[CEU][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11712186	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11712672	0.89[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11713205	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11713248	0.89[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11714392	0.90[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11714422	0.90[CEU][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11715407	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11715435	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11715615	0.90[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11716197	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11716388	0.89[CEU][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11716415	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11717424	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11717902	0.89[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11718050	0.90[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11718234	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11718255	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11719366	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11719585	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11719687	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11720825	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16840594	0.82[EUR][1000 genomes]
rs16840595	0.85[EUR][1000 genomes]
rs17301253	0.90[CEU][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17301521	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17301766	0.84[CEU][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17301889	0.90[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17373504	0.90[CEU][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17373726	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2718801	0.82[CEU][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28846461	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55729127	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55741097	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56040719	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56292037	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56323915	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62280563	0.82[AMR][1000 genomes]
rs62282385	0.81[AMR][1000 genomes]
rs62282388	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62282389	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62282390	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62282392	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62282415	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62282417	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62282418	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62282419	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62282420	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62282421	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62282424	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62282425	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62282427	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62282428	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62282429	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62282431	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62282451	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62282452	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62282453	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62282454	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62282456	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62284060	0.82[AMR][1000 genomes]
rs6765265	0.83[EUR][1000 genomes]
rs7349558	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7630957	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs7650725	0.88[EUR][1000 genomes]
rs7653808	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133365600-133380200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:133378200-133381400	Active TSS	GM12878-XiMat	blood
3	chr3:133378800-133380200	Enhancers	Sigmoid Colon	Sigmoid Colon
4	chr3:133379000-133380200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:133379000-133380200	Flanking Active TSS	HUVEC	blood vessel
6	chr3:133379000-133380600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:133379000-133381000	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr3:133379000-133381200	Active TSS	Fetal Brain Female	brain
9	chr3:133379000-133381600	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr3:133379200-133380400	Flanking Active TSS	Primary hematopoietic stem cells	blood
11	chr3:133379200-133381600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:133379200-133381600	Active TSS	Brain Germinal Matrix	brain
13	chr3:133379400-133380200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:133379400-133380200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:133379400-133380400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr3:133379400-133381000	Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr3:133379400-133381200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:133379400-133381200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:133379400-133381200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:133379400-133381200	Active TSS	NHEK	skin
21	chr3:133379400-133381400	Active TSS	NHLF	lung
22	chr3:133379400-133381600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:133379400-133381600	Active TSS	A549	lung
24	chr3:133379400-133381600	Active TSS	NHDF-Ad	bronchial
25	chr3:133379600-133380200	Active TSS	HepG2	liver
26	chr3:133379600-133380400	Flanking Active TSS	Primary T cells from cord blood	blood
27	chr3:133379600-133380400	Flanking Active TSS	Duodenum Mucosa	Duodenum
28	chr3:133379600-133380400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
29	chr3:133379600-133381000	Active TSS	H1 Cell Line	embryonic stem cell
30	chr3:133379600-133381200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr3:133379600-133381200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:133379600-133381200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr3:133379600-133381200	Active TSS	Fetal Muscle Leg	muscle
34	chr3:133379600-133381200	Active TSS	Fetal Thymus	thymus
35	chr3:133379600-133381400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr3:133379600-133381600	Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr3:133379600-133381600	Active TSS	HSMM	muscle
38	chr3:133379600-133381800	Active TSS	HUES6 Cell Line	embryonic stem cell
39	chr3:133379600-133381800	Active TSS	K562	blood
40	chr3:133379800-133380200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr3:133379800-133380200	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr3:133379800-133380200	Flanking Active TSS	Osteobl	bone
43	chr3:133379800-133380400	Flanking Active TSS	Primary B cells from cord blood	blood
44	chr3:133379800-133380400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr3:133379800-133380400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
46	chr3:133379800-133380400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
47	chr3:133379800-133380400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
48	chr3:133379800-133380400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr3:133379800-133380400	Flanking Active TSS	Brain Angular Gyrus	brain
50	chr3:133379800-133380400	Flanking Active TSS	Fetal Lung	lung

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