Variant report

Variant	rs11154002
Chromosome Location	chr6:121500150-121500151
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:121495458..121497370-chr6:121499505..121502108,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10457413	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10457414	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10457415	0.81[EUR][1000 genomes]
rs10499106	0.82[EUR][1000 genomes]
rs10499109	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs11153999	0.92[CEU][hapmap];0.83[CHB][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11154001	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11154005	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11154012	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs11759795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12191616	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12192398	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12198421	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12206641	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12212646	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13199297	1.00[ASW][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap]
rs17644324	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28877073	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs407630	1.00[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs421242	0.84[EUR][1000 genomes]
rs7745023	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs9387918	0.96[CEU][hapmap];0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][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	nsv1023384	chr6:121235867-121683448	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv530527	chr6:121298528-121789855	ZNF genes & repeats Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv604572	chr6:121465011-121544876	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:121474600-121508600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:121475600-121508600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr6:121478800-121535400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr6:121479000-121505000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr6:121479200-121502600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr6:121479600-121501400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr6:121480200-121502400	Weak transcription	Left Ventricle	heart
8	chr6:121480200-121504600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr6:121480200-121535600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr6:121480400-121505400	Weak transcription	Adipose Nuclei	Adipose
11	chr6:121480600-121501000	Weak transcription	Brain Hippocampus Middle	brain
12	chr6:121480600-121502200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr6:121480800-121535400	Weak transcription	Fetal Intestine Large	intestine
14	chr6:121481000-121502600	Weak transcription	Primary B cells from peripheral blood	blood
15	chr6:121481000-121535400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr6:121487400-121556000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr6:121494600-121516600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr6:121495200-121502200	Weak transcription	Brain Substantia Nigra	brain
19	chr6:121495200-121529400	Weak transcription	Primary B cells from cord blood	blood
20	chr6:121496400-121516600	Weak transcription	Fetal Muscle Trunk	muscle
21	chr6:121496800-121535400	Weak transcription	Fetal Lung	lung
22	chr6:121498000-121502600	Weak transcription	Fetal Brain Male	brain
23	chr6:121498000-121518000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr6:121498200-121500200	Strong transcription	Primary T cells from cord blood	blood
25	chr6:121498400-121504400	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr6:121498600-121500200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr6:121498600-121502400	Weak transcription	Fetal Stomach	stomach
28	chr6:121498600-121535400	Weak transcription	Pancreas	Pancrea
29	chr6:121498800-121500200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr6:121499000-121516000	Weak transcription	Aorta	Aorta
31	chr6:121499200-121500200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr6:121499200-121500200	ZNF genes & repeats	Dnd41	blood
33	chr6:121499200-121509000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr6:121499600-121503000	Weak transcription	Brain Angular Gyrus	brain
35	chr6:121499800-121500200	Strong transcription	Ovary	ovary
36	chr6:121499800-121502200	Weak transcription	GM12878-XiMat	blood
37	chr6:121499800-121535800	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr6:121500000-121504800	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr6:121500000-121529000	Weak transcription	Primary T helper cells fromperipheralblood	blood

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