Variant report

Variant	rs2278450
Chromosome Location	chr2:47183650-47183651
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47168340..47172583-chr2:47183123..47189203,6	MCF-7	breast:
2	chr2:47182254..47183796-chr2:47260379..47263312,2	MCF-7	breast:
3	chr2:47182193..47183883-chr2:47197911..47200319,2	K562	blood:
4	chr2:47174154..47179572-chr2:47181486..47185069,4	MCF-7	breast:
5	chr2:47181119..47183669-chr2:47402137..47404720,3	K562	blood:

Variant related genes	Relation type
ENSG00000180398	Chromatin interaction
ENSG00000068724	Chromatin interaction
ENSG00000143933	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10495941	0.95[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10779934	0.85[JPT][hapmap]
rs11125103	0.96[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11125104	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1122516	0.91[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes]
rs11680492	0.91[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11685461	0.91[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12712980	0.91[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12712981	0.91[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12712982	0.87[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12712984	0.81[CEU][hapmap];0.88[JPT][hapmap]
rs1865258	0.84[JPT][hapmap]
rs1865261	0.87[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2278449	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28434195	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28694585	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4952857	0.96[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4953437	0.91[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4953438	0.91[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6544943	0.87[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6544944	0.91[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6713810	0.91[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6727651	0.91[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs735888	0.89[JPT][hapmap]
rs7557193	0.87[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes]
rs7602813	0.87[CEU][hapmap];0.80[CHB][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes]
rs892380	0.91[CEU][hapmap];0.80[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
5	nsv524970	chr2:47162739-47302095	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47169800-47214600	Weak transcription	Fetal Kidney	kidney
2	chr2:47170800-47184000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:47173000-47191800	Weak transcription	Fetal Brain Male	brain
4	chr2:47173400-47184000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr2:47174200-47183800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr2:47174200-47184200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr2:47174400-47212400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr2:47176400-47192600	Strong transcription	Dnd41	blood
9	chr2:47177200-47185000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr2:47177200-47210400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr2:47177400-47192800	Strong transcription	Fetal Stomach	stomach
12	chr2:47177600-47188200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr2:47177600-47190000	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr2:47177600-47191200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr2:47178400-47183800	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr2:47178400-47183800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr2:47178400-47188000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr2:47178400-47192800	Strong transcription	Thymus	Thymus
19	chr2:47178600-47183800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr2:47178600-47189800	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr2:47178800-47189400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr2:47178800-47190000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr2:47178800-47191400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr2:47179000-47188200	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr2:47179000-47191000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr2:47179000-47192800	Strong transcription	Primary T cells from cord blood	blood
27	chr2:47179200-47195000	Strong transcription	Fetal Thymus	thymus
28	chr2:47179400-47183800	Weak transcription	Gastric	stomach
29	chr2:47179400-47184200	Weak transcription	Brain Germinal Matrix	brain
30	chr2:47179400-47189600	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr2:47179400-47191400	Strong transcription	Primary hematopoietic stem cells	blood
32	chr2:47179400-47192200	Strong transcription	Primary B cells from cord blood	blood
33	chr2:47179400-47192600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr2:47179400-47193800	Strong transcription	Primary B cells from peripheral blood	blood
35	chr2:47179800-47189400	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr2:47180000-47184000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr2:47180000-47184200	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr2:47180800-47188000	Strong transcription	Fetal Lung	lung
39	chr2:47181200-47192200	Strong transcription	GM12878-XiMat	blood
40	chr2:47181400-47183800	Enhancers	Stomach Mucosa	stomach
41	chr2:47181400-47184400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr2:47181600-47183800	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr2:47181600-47210800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr2:47181800-47184000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr2:47181800-47185800	Enhancers	Liver	Liver
46	chr2:47182000-47184000	Enhancers	Pancreas	Pancrea
47	chr2:47182200-47184600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr2:47182600-47183800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr2:47182600-47184000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr2:47182600-47187200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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