Variant report

Variant	rs490860
Chromosome Location	chr11:102349158-102349159
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:102320074..102325014-chr11:102347034..102351660,6	MCF-7	breast:
2	chr11:102349024..102351373-chr11:102352689..102355274,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000255337	Chromatin interaction
ENSG00000152558	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs2019777	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2156530	0.89[CEU][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs480846	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs518851	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs530227	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs539751	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs548841	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs548974	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs557747	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs558679	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs567670	0.81[YRI][hapmap]
rs589271	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs602271	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs621010	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs650411	0.98[EUR][1000 genomes]
rs651853	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs652329	0.80[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs666042	0.87[EUR][1000 genomes]
rs683933	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035567	chr11:102264516-102431607	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv898334	chr11:102272884-102353192	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv469990	chr11:102335609-102413943	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv556150	chr11:102335609-102415859	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv468854	chr11:102336617-102413943	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv556151	chr11:102336617-102413943	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 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	chr11:102341000-102359600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr11:102345000-102349200	Weak transcription	Colonic Mucosa	Colon
3	chr11:102345000-102351600	Weak transcription	Gastric	stomach
4	chr11:102346800-102350000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr11:102346800-102350400	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr11:102346800-102350600	Enhancers	Primary T cells from cord blood	blood
7	chr11:102347000-102350400	Enhancers	Fetal Intestine Small	intestine
8	chr11:102347000-102353000	Enhancers	Stomach Mucosa	stomach
9	chr11:102347600-102350200	Enhancers	HepG2	liver
10	chr11:102347800-102349200	Weak transcription	Fetal Kidney	kidney
11	chr11:102347800-102349400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr11:102347800-102349400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr11:102347800-102349400	Weak transcription	Colon Smooth Muscle	Colon
14	chr11:102347800-102353000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr11:102348000-102349200	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr11:102348000-102349200	Weak transcription	Duodenum Mucosa	Duodenum
17	chr11:102348000-102349600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr11:102348000-102353400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr11:102348200-102349200	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr11:102348200-102349200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr11:102348200-102349200	Weak transcription	Primary hematopoietic stem cells	blood
22	chr11:102348200-102349200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr11:102348200-102349200	Weak transcription	Fetal Intestine Large	intestine
24	chr11:102348200-102349200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr11:102348200-102349400	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr11:102348200-102349400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr11:102348200-102349400	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr11:102348200-102349400	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr11:102348200-102349800	Weak transcription	Brain Anterior Caudate	brain
30	chr11:102348200-102351400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr11:102348200-102351800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr11:102348600-102351600	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr11:102348800-102350000	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr11:102348800-102350000	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr11:102348800-102350200	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr11:102348800-102350800	Enhancers	Brain Germinal Matrix	brain
37	chr11:102348800-102352000	Weak transcription	K562	blood
38	chr11:102348800-102353400	Weak transcription	Hela-S3	cervix
39	chr11:102349000-102349400	Enhancers	Primary T killer memory cells from peripheral blood	blood

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