Variant report

Variant	rs1408035
Chromosome Location	chr11:34475749-34475750
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	E2F4	chr11:34475711-34475861	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:34459364..34461462-chr11:34473954..34476897,2	MCF-7	breast:
2	chr11:34475298..34477480-chr11:34481410..34482936,2	K562	blood:
3	chr11:34072099..34074725-chr11:34473129..34475989,2	MCF-7	breast:

Variant related genes	Relation type
CAT	TF binding region
ENSG00000121691	Chromatin interaction
ENSG00000135387	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10836244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2284365	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2284367	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2284368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2284369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2420388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3758733	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3781711	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4755372	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4755373	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4756148	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4756153	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs554576	0.83[ASN][1000 genomes]
rs566979	0.87[CHB][hapmap]
rs6484722	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7113917	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs769217	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs769218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7928213	0.89[ASN][1000 genomes]
rs942223	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][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	nsv897205	chr11:34248229-34507213	Enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv897207	chr11:34253683-34621004	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv897208	chr11:34257064-34562247	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv897209	chr11:34309519-34548906	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv832114	chr11:34424428-34607851	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1408035	CAT	cis	Whole Blood	GTEx
rs1408035	CAT	Cis_1M	lymphoblastoid	RTeQTL
rs1408035	CAT	cis	Artery Tibial	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:34461400-34482800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:34461800-34485800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr11:34462000-34477600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr11:34466000-34479000	Weak transcription	Small Intestine	intestine
5	chr11:34468000-34481000	Weak transcription	Stomach Mucosa	stomach
6	chr11:34469800-34479000	Strong transcription	HepG2	liver
7	chr11:34469800-34487400	Strong transcription	Hela-S3	cervix
8	chr11:34470200-34486600	Genic enhancers	Liver	Liver
9	chr11:34470400-34475800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr11:34470400-34482800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr11:34470400-34487400	Strong transcription	Sigmoid Colon	Sigmoid Colon
12	chr11:34470600-34476000	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr11:34470600-34476400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr11:34470800-34476000	Strong transcription	Brain Anterior Caudate	brain
15	chr11:34470800-34476200	Strong transcription	K562	blood
16	chr11:34470800-34488000	Strong transcription	Brain Hippocampus Middle	brain
17	chr11:34470800-34488000	Strong transcription	Fetal Intestine Large	intestine
18	chr11:34470800-34494200	Strong transcription	Brain Germinal Matrix	brain
19	chr11:34470800-34495600	Strong transcription	Stomach Smooth Muscle	stomach
20	chr11:34471000-34478600	Strong transcription	GM12878-XiMat	blood
21	chr11:34471000-34481400	Strong transcription	Fetal Lung	lung
22	chr11:34471000-34485400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr11:34471000-34487200	Strong transcription	Primary B cells from peripheral blood	blood
24	chr11:34471000-34487400	Strong transcription	Osteobl	bone
25	chr11:34471000-34494000	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr11:34471200-34479600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr11:34471200-34481200	Strong transcription	Fetal Brain Female	brain
28	chr11:34471200-34483400	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr11:34471200-34487000	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr11:34471400-34475800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr11:34471400-34475800	Strong transcription	Skeletal Muscle Male	skeletal muscle
32	chr11:34471400-34475800	Strong transcription	HUVEC	blood vessel
33	chr11:34471400-34475800	Strong transcription	NHLF	lung
34	chr11:34471400-34476200	Strong transcription	Colonic Mucosa	Colon
35	chr11:34471400-34476400	Strong transcription	NH-A	brain
36	chr11:34471400-34476800	Strong transcription	Rectal Smooth Muscle	rectum
37	chr11:34471400-34477000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr11:34471400-34478600	Strong transcription	Muscle Satellite Cultured Cells	--
39	chr11:34471400-34480200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr11:34471400-34481000	Strong transcription	Left Ventricle	heart
41	chr11:34471400-34481400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr11:34471400-34481600	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr11:34471400-34481800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr11:34471400-34486400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr11:34471400-34486600	Strong transcription	Primary T cells from cord blood	blood
46	chr11:34471400-34487000	Strong transcription	Thymus	Thymus
47	chr11:34471400-34487200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr11:34471400-34487200	Strong transcription	Fetal Muscle Trunk	muscle
49	chr11:34471400-34487400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr11:34471400-34487400	Strong transcription	Ovary	ovary

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