Variant report

Variant	rs12417295
Chromosome Location	chr11:100850800-100850801
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:100850328..100852542-chr11:100997954..101000067,2	MCF-7	breast:
2	chr11:100850533..100851521-chr11:100874106..100874843,2	MCF-7	breast:
3	chr11:100849467..100854913-chr11:100993227..101000778,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000082175	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12416898	1.00[EUR][1000 genomes]
rs12417055	0.81[EUR][1000 genomes]
rs12417366	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12417367	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12417750	1.00[CEU][hapmap]
rs12417981	1.00[EUR][1000 genomes]
rs12418330	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12418344	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12418450	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12418561	1.00[EUR][1000 genomes]
rs12418769	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12419150	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12419214	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12420084	1.00[EUR][1000 genomes]
rs12420294	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs12420453	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12420466	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12420698	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.87[MKK][hapmap];0.83[TSI][hapmap];1.00[EUR][1000 genomes]
rs12420922	1.00[EUR][1000 genomes]
rs12421386	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12421655	0.81[EUR][1000 genomes]
rs12422140	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1943499	0.81[EUR][1000 genomes]
rs2186784	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2277274	1.00[EUR][1000 genomes]
rs2277275	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2407822	0.81[EUR][1000 genomes]
rs28492796	1.00[EUR][1000 genomes]
rs3843607	1.00[EUR][1000 genomes]
rs3886266	1.00[EUR][1000 genomes]
rs4587692	0.81[EUR][1000 genomes]
rs60423120	1.00[EUR][1000 genomes]
rs60612076	1.00[EUR][1000 genomes]
rs61995873	0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048356	chr11:100713096-101058995	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv541154	chr11:100713096-101058995	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:100810000-100852200	Weak transcription	Small Intestine	intestine
2	chr11:100830600-100858200	Weak transcription	Colonic Mucosa	Colon
3	chr11:100834400-100851600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr11:100841600-100852200	Weak transcription	Spleen	Spleen
5	chr11:100841800-100852200	Weak transcription	Esophagus	oesophagus
6	chr11:100844000-100860200	Strong transcription	Placenta	Placenta
7	chr11:100844800-100863000	Weak transcription	Brain Anterior Caudate	brain
8	chr11:100845800-100850800	Weak transcription	K562	blood
9	chr11:100846200-100857400	Weak transcription	Fetal Brain Male	brain
10	chr11:100846400-100855200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr11:100846800-100851200	Weak transcription	Brain Hippocampus Middle	brain
12	chr11:100847000-100855200	Weak transcription	Primary B cells from peripheral blood	blood
13	chr11:100847800-100852200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr11:100847800-100854400	Weak transcription	Right Ventricle	heart
15	chr11:100848000-100851800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr11:100848000-100861800	Weak transcription	Fetal Heart	heart
17	chr11:100848200-100850800	Weak transcription	Fetal Muscle Trunk	muscle
18	chr11:100848200-100851600	Weak transcription	Ovary	ovary
19	chr11:100848200-100856200	Weak transcription	Fetal Intestine Small	intestine
20	chr11:100848200-100856400	Weak transcription	Fetal Stomach	stomach
21	chr11:100848200-100857400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr11:100848200-100858600	Weak transcription	Gastric	stomach
23	chr11:100848200-100859600	Weak transcription	Stomach Mucosa	stomach
24	chr11:100848200-100861200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr11:100848200-100866000	Weak transcription	Psoas Muscle	Psoas
26	chr11:100848400-100851800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr11:100848400-100852400	Weak transcription	Primary T cells from cord blood	blood
28	chr11:100848400-100859800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr11:100848400-100859800	Weak transcription	Fetal Kidney	kidney
30	chr11:100848400-100860800	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr11:100848400-100863200	Weak transcription	Fetal Intestine Large	intestine
32	chr11:100848400-100864600	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr11:100848600-100852800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr11:100848600-100859200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr11:100848600-100863400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr11:100848600-100865200	Weak transcription	Left Ventricle	heart
37	chr11:100848600-100865800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr11:100848800-100855000	Weak transcription	Primary B cells from cord blood	blood
39	chr11:100848800-100857600	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr11:100848800-100858000	Weak transcription	Duodenum Mucosa	Duodenum
41	chr11:100848800-100860000	Weak transcription	NH-A	brain
42	chr11:100848800-100864800	Weak transcription	HSMM	muscle
43	chr11:100849000-100852200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr11:100849000-100862000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr11:100849000-100863000	Weak transcription	Stomach Smooth Muscle	stomach
46	chr11:100849200-100867400	Weak transcription	Fetal Lung	lung
47	chr11:100849600-100851000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
48	chr11:100849600-100856200	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr11:100849800-100851200	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr11:100849800-100856400	Weak transcription	Rectal Mucosa Donor 31	rectum

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