Variant report

Variant	rs2251216
Chromosome Location	chr3:59795925-59795926
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	chr3:59560988..59561827-chr3:59795202..59795948,3	MCF-7	breast:
2	chr3:59593056..59594000-chr3:59795106..59795983,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11720016	0.90[ASN][1000 genomes]
rs12494457	0.89[ASN][1000 genomes]
rs12634148	1.00[CHB][hapmap];0.82[CHD][hapmap]
rs13434180	0.91[CEU][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2629877	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3100803	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3112505	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4679507	0.91[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap]
rs497767	0.93[ASN][1000 genomes]
rs505780	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs534185	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.91[ASN][1000 genomes]
rs565226	0.94[CEU][hapmap]
rs590581	0.86[CEU][hapmap];0.95[CHB][hapmap]
rs591947	0.86[ASN][1000 genomes]
rs605545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9846213	1.00[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]

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	nsv1014601	chr3:59666609-59888166	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
2	nsv1003387	chr3:59756364-59831340	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv460562	chr3:59760118-59826778	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv590381	chr3:59760118-59826778	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv460563	chr3:59772342-59827390	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv590383	chr3:59772342-59827390	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv428085	chr3:59782509-60070116	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2251216	ID2B	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:59770400-59825200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr3:59778200-59811200	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr3:59787200-59802000	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr3:59788400-59797600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:59789400-59796800	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr3:59789400-59797600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr3:59789400-59797600	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr3:59789800-59797800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr3:59789800-59798000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:59791400-59797800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr3:59793000-59799600	Enhancers	Brain Germinal Matrix	brain
12	chr3:59794000-59796800	Enhancers	Fetal Stomach	stomach
13	chr3:59794000-59797000	Enhancers	Fetal Thymus	thymus
14	chr3:59794000-59798400	Enhancers	Fetal Muscle Leg	muscle
15	chr3:59794200-59796000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:59794200-59798200	Enhancers	HSMMtube	muscle
17	chr3:59794200-59800800	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr3:59794400-59796000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:59794800-59796000	Enhancers	Brain Hippocampus Middle	brain
20	chr3:59795000-59796000	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr3:59795000-59796800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr3:59795000-59797000	Enhancers	Brain Angular Gyrus	brain
23	chr3:59795200-59796400	Weak transcription	NHDF-Ad	bronchial
24	chr3:59795200-59798000	Enhancers	Fetal Brain Female	brain
25	chr3:59795400-59796000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:59795400-59796000	Enhancers	Brain Cingulate Gyrus	brain
27	chr3:59795400-59796000	Enhancers	Right Atrium	heart
28	chr3:59795400-59796200	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr3:59795400-59796200	Enhancers	Fetal Muscle Trunk	muscle
30	chr3:59795400-59796400	Enhancers	Brain Anterior Caudate	brain
31	chr3:59795400-59796400	Enhancers	Dnd41	blood
32	chr3:59795400-59796600	Enhancers	Thymus	Thymus
33	chr3:59795400-59798800	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr3:59795400-59800000	Enhancers	Fetal Brain Male	brain
35	chr3:59795600-59796200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr3:59795600-59796400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:59795600-59797600	Weak transcription	NH-A	brain
38	chr3:59795600-59797800	Weak transcription	HSMM	muscle
39	chr3:59795600-59798000	Weak transcription	Osteobl	bone
40	chr3:59795600-59798600	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr3:59795800-59796000	Enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr3:59795800-59796000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr3:59795800-59796000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr3:59795800-59796000	Enhancers	Aorta	Aorta
45	chr3:59795800-59796200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr3:59795800-59796200	Enhancers	Primary T cells fromperipheralblood	blood
47	chr3:59795800-59796200	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr3:59795800-59796400	Enhancers	Stomach Mucosa	stomach
49	chr3:59795800-59796800	Enhancers	Primary T cells from cord blood	blood
50	chr3:59795800-59796800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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