Variant report

Variant	rs2574980
Chromosome Location	chr10:52072912-52072913
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:52063071..52064625-chr10:52072402..52074193,2	MCF-7	breast:
2	chr10:52062509..52064058-chr10:52071657..52073815,2	K562	blood:
3	chr10:52069285..52071040-chr10:52072375..52074305,2	K562	blood:
4	chr10:52064687..52067489-chr10:52072620..52075726,3	K562	blood:
5	chr10:52071869..52074741-chr10:52080323..52082329,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12569679	1.00[EUR][1000 genomes]
rs1436210	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17179735	1.00[EUR][1000 genomes]
rs17179784	1.00[EUR][1000 genomes]
rs17179881	1.00[EUR][1000 genomes]
rs2140407	0.86[ASN][1000 genomes]
rs2304444	0.90[CHB][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap]
rs2574978	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[ASN][1000 genomes]
rs2688880	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2688881	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2688886	0.98[ASN][1000 genomes]
rs2842087	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2842088	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2842089	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2842090	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2842091	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2842092	0.98[ASN][1000 genomes]
rs2842093	0.88[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs2842094	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2842095	0.97[ASN][1000 genomes]
rs2842097	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4540795	1.00[EUR][1000 genomes]
rs59510112	1.00[EUR][1000 genomes]
rs72634643	1.00[EUR][1000 genomes]
rs7919474	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518071	chr10:51595893-52157935	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1053903	chr10:51886486-52163991	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1040661	chr10:51886486-52164585	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1051028	chr10:51886486-52164585	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1037118	chr10:51886486-52167442	Enhancers ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	esv2830205	chr10:51978430-52135215	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
12	nsv1053293	chr10:51981959-52102649	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
13	nsv1046850	chr10:52009869-52135542	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
14	nsv540625	chr10:52009869-52135542	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
15	esv2762864	chr10:52030945-52107415	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
16	nsv521273	chr10:52051645-52197847	Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52061400-52080400	Weak transcription	Psoas Muscle	Psoas
2	chr10:52062200-52075000	Weak transcription	HUVEC	blood vessel
3	chr10:52063200-52076600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr10:52064000-52073400	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr10:52064600-52073000	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr10:52065000-52081600	Weak transcription	Stomach Mucosa	stomach
7	chr10:52065200-52073000	Weak transcription	Fetal Thymus	thymus
8	chr10:52065200-52076800	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr10:52065400-52073000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr10:52065400-52073000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr10:52065400-52077000	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr10:52065600-52075000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr10:52066200-52073000	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr10:52066400-52073000	Strong transcription	Primary T cells from cord blood	blood
15	chr10:52067000-52075400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr10:52067400-52093600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr10:52068000-52074400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr10:52068200-52080400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr10:52069200-52075000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr10:52069200-52076400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr10:52069400-52075800	Weak transcription	Fetal Brain Female	brain
22	chr10:52070000-52081400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr10:52070800-52075000	Weak transcription	Fetal Brain Male	brain
24	chr10:52071000-52074600	Weak transcription	Colon Smooth Muscle	Colon
25	chr10:52071000-52075200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr10:52071000-52081400	Weak transcription	NH-A	brain
27	chr10:52071000-52083600	Weak transcription	Primary B cells from cord blood	blood
28	chr10:52071000-52084200	Weak transcription	Spleen	Spleen
29	chr10:52071000-52084800	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr10:52071000-52085000	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr10:52071000-52085200	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr10:52071000-52085400	Weak transcription	Pancreas	Pancrea
33	chr10:52071000-52085800	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr10:52071000-52102400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr10:52071000-52102600	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr10:52071200-52073000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr10:52071200-52073600	Weak transcription	NHLF	lung
38	chr10:52071200-52074000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr10:52071200-52074400	Weak transcription	Left Ventricle	heart
40	chr10:52071200-52074400	Weak transcription	Ovary	ovary
41	chr10:52071200-52074600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr10:52071200-52074600	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr10:52071200-52075000	Weak transcription	Brain Anterior Caudate	brain
44	chr10:52071200-52075000	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr10:52071200-52075000	Weak transcription	GM12878-XiMat	blood
46	chr10:52071200-52075200	Weak transcription	Fetal Stomach	stomach
47	chr10:52071200-52076000	Weak transcription	Fetal Muscle Trunk	muscle
48	chr10:52071200-52076000	Weak transcription	Gastric	stomach
49	chr10:52071200-52076000	Weak transcription	Stomach Smooth Muscle	stomach
50	chr10:52071200-52077000	Weak transcription	HSMM	muscle

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