Variant report

Variant	rs13009447
Chromosome Location	chr2:55897996-55897997
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55843805..55846748-chr2:55896170..55899222,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138041	Chromatin interaction
ENSG00000272606	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1013138	0.83[CHB][hapmap]
rs10207590	0.86[ASN][1000 genomes]
rs12329050	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12467339	0.83[AMR][1000 genomes]
rs12473585	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12473621	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12617627	0.89[CHB][hapmap];0.91[YRI][hapmap]
rs12617719	0.88[ASN][1000 genomes]
rs12618859	0.91[YRI][hapmap]
rs12619903	0.83[CHB][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12620407	0.82[ASN][1000 genomes]
rs12992408	0.89[CHB][hapmap];0.85[YRI][hapmap]
rs12992827	0.87[CHB][hapmap]
rs12993624	0.82[YRI][hapmap]
rs12999966	0.89[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13001425	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13002860	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13007577	0.82[AFR][1000 genomes]
rs13009239	0.82[ASN][1000 genomes]
rs13009906	0.89[CHB][hapmap];0.81[JPT][hapmap];0.85[YRI][hapmap]
rs13010217	0.91[YRI][hapmap]
rs13013133	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13013699	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13014898	0.89[CHB][hapmap];0.86[YRI][hapmap]
rs13015018	0.94[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs13015030	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs13021958	0.83[YRI][hapmap]
rs13024761	0.80[AMR][1000 genomes]
rs13025331	0.91[YRI][hapmap]
rs13032503	0.89[CHB][hapmap];0.81[JPT][hapmap];0.85[YRI][hapmap]
rs1318672	0.89[CHB][hapmap]
rs1443746	0.83[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes]
rs17800203	0.83[CHB][hapmap]
rs1822513	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34513671	0.82[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs34679603	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3791654	0.86[YRI][hapmap]
rs4322879	0.91[YRI][hapmap]
rs5012561	0.83[CHB][hapmap];0.83[JPT][hapmap];0.86[YRI][hapmap]
rs56122729	0.87[ASN][1000 genomes]
rs6737995	0.91[YRI][hapmap]
rs6757006	0.83[CHB][hapmap];0.83[JPT][hapmap];0.86[YRI][hapmap]
rs7575170	0.94[CHB][hapmap];0.88[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7592219	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7596377	0.83[ASN][1000 genomes]
rs8080	0.89[CHB][hapmap];0.81[JPT][hapmap];0.80[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers 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 miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv834080	chr2:55741036-55927928	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	esv2757798	chr2:55747239-55981074	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv2759050	chr2:55747239-55981074	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv1008452	chr2:55809191-55987274	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	esv2762645	chr2:55892248-55963418	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55846800-55919800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:55847400-55911000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:55858200-55920400	Weak transcription	Fetal Heart	heart
4	chr2:55860400-55905400	Weak transcription	Fetal Brain Male	brain
5	chr2:55864400-55919600	Weak transcription	NHLF	lung
6	chr2:55866600-55920000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr2:55870400-55920000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:55870600-55920000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr2:55870800-55903600	Weak transcription	Gastric	stomach
10	chr2:55870800-55909000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:55870800-55920400	Weak transcription	Aorta	Aorta
12	chr2:55871000-55920000	Weak transcription	Spleen	Spleen
13	chr2:55871200-55905200	Weak transcription	Brain Angular Gyrus	brain
14	chr2:55871400-55905200	Weak transcription	Fetal Kidney	kidney
15	chr2:55873200-55919800	Weak transcription	Small Intestine	intestine
16	chr2:55873800-55899400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr2:55874800-55920200	Weak transcription	Pancreas	Pancrea
18	chr2:55879000-55917600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr2:55879200-55902800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr2:55879400-55914200	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr2:55881200-55913000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr2:55881800-55898000	Weak transcription	NHDF-Ad	bronchial
23	chr2:55882200-55909600	Weak transcription	Brain Germinal Matrix	brain
24	chr2:55883000-55906800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr2:55883000-55919800	Weak transcription	HSMMtube	muscle
26	chr2:55883200-55906600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr2:55883400-55906800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr2:55885600-55902600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr2:55887600-55898400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:55887800-55900200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr2:55887800-55900400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr2:55888000-55907200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr2:55888600-55899600	Weak transcription	Fetal Brain Female	brain
34	chr2:55888600-55904200	Weak transcription	Esophagus	oesophagus
35	chr2:55888800-55905200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr2:55888800-55909600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr2:55889800-55918400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr2:55890200-55902400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr2:55890200-55915600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:55890400-55898400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr2:55890400-55898400	Strong transcription	Hela-S3	cervix
42	chr2:55890400-55914200	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr2:55891400-55900800	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr2:55892000-55903200	Strong transcription	Fetal Thymus	thymus
45	chr2:55892000-55914000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr2:55892200-55914000	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr2:55892400-55901200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr2:55892400-55903200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr2:55892400-55905800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr2:55892400-55919800	Weak transcription	Primary neutrophils fromperipheralblood	blood

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