Variant report

Variant	rs12418601
Chromosome Location	chr11:120052360-120052361
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:120051503..120053390-chr11:120056231..120058404,2	MCF-7	breast:
2	chr11:120049376..120051724-chr11:120052135..120053974,2	K562	blood:
3	chr11:120050542..120053166-chr11:120080425..120082146,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000184232	Chromatin interaction
ENSG00000137699	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11217755	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12419025	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12421142	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2848728	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2851718	0.95[JPT][hapmap]
rs35650539	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4938788	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4938789	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4938791	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs547124	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs582071	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs604413	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61900474	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61900479	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs620602	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs626151	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs657898	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs659912	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs666432	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs673292	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs675647	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7949789	0.90[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054057	chr11:119781953-120519770	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv541178	chr11:119781953-120519770	Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv428581	chr11:120006048-120167603	Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv518464	chr11:120040442-120109967	Genic enhancers Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120043600-120057000	Weak transcription	Esophagus	oesophagus
2	chr11:120044400-120055200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr11:120046200-120053000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr11:120046800-120055800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr11:120048200-120055600	Enhancers	Fetal Stomach	stomach
6	chr11:120049000-120055200	Enhancers	Fetal Muscle Trunk	muscle
7	chr11:120049200-120054400	Genic enhancers	Fetal Intestine Small	intestine
8	chr11:120049400-120054800	Enhancers	Brain Anterior Caudate	brain
9	chr11:120049400-120059800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr11:120049600-120053000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
11	chr11:120049600-120053800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr11:120049600-120057000	Weak transcription	Left Ventricle	heart
13	chr11:120049800-120052800	Weak transcription	Colon Smooth Muscle	Colon
14	chr11:120049800-120053200	Weak transcription	Stomach Mucosa	stomach
15	chr11:120049800-120054200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr11:120049800-120054200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr11:120050000-120052400	Weak transcription	Ovary	ovary
18	chr11:120050000-120053600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr11:120050000-120053800	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr11:120050400-120052800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr11:120050400-120054200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:120051000-120053000	Enhancers	HepG2	liver
23	chr11:120051000-120053800	Enhancers	Liver	Liver
24	chr11:120051000-120054200	Enhancers	Spleen	Spleen
25	chr11:120051200-120053200	Genic enhancers	Fetal Intestine Large	intestine
26	chr11:120051200-120053400	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr11:120051200-120053800	Enhancers	Brain Hippocampus Middle	brain
28	chr11:120051400-120053600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr11:120051400-120053600	Enhancers	Fetal Kidney	kidney
30	chr11:120051600-120052600	Weak transcription	Fetal Lung	lung
31	chr11:120051600-120053000	Enhancers	Brain Angular Gyrus	brain
32	chr11:120051600-120053000	Weak transcription	Small Intestine	intestine
33	chr11:120051600-120054200	Enhancers	Brain Cingulate Gyrus	brain
34	chr11:120051600-120054200	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr11:120051600-120055400	Weak transcription	Gastric	stomach
36	chr11:120051600-120057600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr11:120051800-120052800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr11:120051800-120053000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr11:120051800-120053800	Weak transcription	Right Ventricle	heart
40	chr11:120051800-120054600	Enhancers	Pancreas	Pancrea
41	chr11:120051800-120057000	Weak transcription	HMEC	breast
42	chr11:120051800-120057200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr11:120052000-120052800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
44	chr11:120052000-120052800	Weak transcription	Duodenum Mucosa	Duodenum
45	chr11:120052000-120053000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr11:120052000-120053000	Weak transcription	Right Atrium	heart
47	chr11:120052000-120053400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr11:120052000-120054200	Enhancers	Brain Germinal Matrix	brain
49	chr11:120052000-120055600	Weak transcription	Osteobl	bone
50	chr11:120052000-120055800	Weak transcription	Fetal Brain Male	brain

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