Variant report

Variant	rs12571538
Chromosome Location	chr10:6178961-6178962
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:6175564..6180792-chr10:6183747..6189034,7	MCF-7	breast:
2	chr10:6171306..6174580-chr10:6176089..6182503,5	MCF-7	breast:
3	chr10:6178646..6179311-chr5:179268532..179269425,2	MCF-7	breast:
4	chr10:6178289..6180326-chr10:6204239..6205826,2	K562	blood:
5	chr10:6175966..6181179-chr10:6182519..6187998,8	K562	blood:

Variant related genes	Relation type
ENSG00000170525	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10400124	1.00[JPT][hapmap]
rs10400125	1.00[JPT][hapmap]
rs10400165	1.00[JPT][hapmap]
rs11256953	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11256954	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11256957	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12219630	1.00[JPT][hapmap]
rs1887028	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1887031	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3920615	0.94[JPT][hapmap]
rs4291580	0.87[AMR][1000 genomes]
rs4747887	1.00[JPT][hapmap]
rs4747888	1.00[JPT][hapmap]
rs4750012	1.00[JPT][hapmap]
rs4750016	0.81[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs61839724	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7099083	0.94[JPT][hapmap]
rs7476043	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs943122	0.81[AMR][1000 genomes];0.89[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	esv34061	chr10:5726821-6225187	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv1040721	chr10:6155144-6322566	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv540476	chr10:6155144-6322566	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv1054044	chr10:6155144-6487217	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv894816	chr10:6173416-6190343	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv894817	chr10:6173416-6251252	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6171400-6183200	Weak transcription	Right Atrium	heart
2	chr10:6172200-6182800	Weak transcription	Brain Angular Gyrus	brain
3	chr10:6172400-6181600	Weak transcription	Spleen	Spleen
4	chr10:6172400-6182200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr10:6173000-6181000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr10:6176200-6179200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr10:6176200-6179200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
8	chr10:6176400-6179400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr10:6176600-6179000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr10:6176600-6185000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr10:6176800-6179400	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr10:6176800-6182000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr10:6177200-6181400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr10:6177200-6181600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr10:6177200-6181800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr10:6177200-6182000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr10:6177600-6179000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr10:6177600-6179200	Flanking Active TSS	GM12878-XiMat	blood
19	chr10:6177600-6179600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
20	chr10:6177800-6179400	Enhancers	NHDF-Ad	bronchial
21	chr10:6178000-6179000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr10:6178000-6179200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr10:6178000-6179400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr10:6178000-6179400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr10:6178000-6179400	Enhancers	NHLF	lung
26	chr10:6178200-6179000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr10:6178200-6179000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr10:6178200-6179000	Flanking Active TSS	Osteobl	bone
29	chr10:6178200-6179200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr10:6178200-6179200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr10:6178200-6179200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr10:6178200-6179200	Enhancers	Esophagus	oesophagus
33	chr10:6178200-6179400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr10:6178200-6179400	Enhancers	HMEC	breast
35	chr10:6178200-6182000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr10:6178400-6179000	Enhancers	H1 Cell Line	embryonic stem cell
37	chr10:6178400-6179000	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr10:6178400-6179000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
39	chr10:6178400-6179000	Flanking Active TSS	NHEK	skin
40	chr10:6178400-6179200	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr10:6178400-6179400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
42	chr10:6178400-6179400	Enhancers	Adipose Nuclei	Adipose
43	chr10:6178600-6179000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr10:6178600-6179000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr10:6178600-6179000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
46	chr10:6178600-6179400	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr10:6178600-6182000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr10:6178800-6179000	Enhancers	A549	lung
49	chr10:6178800-6179200	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr10:6178800-6179200	Enhancers	HSMM	muscle

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