Variant report

Variant	rs12573401
Chromosome Location	chr10:90148796-90148797
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:89631936..89633868-chr10:90147243..90149574,2	MCF-7	breast:
2	chr10:90020897..90023455-chr10:90147656..90149656,2	MCF-7	breast:
3	chr10:89619905..89627532-chr10:90145841..90152433,14	MCF-7	breast:
4	chr10:89619429..89620951-chr10:90148728..90149780,5	MCF-7	breast:
5	chr10:89618790..89627859-chr10:90143252..90153362,36	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171862	Chromatin interaction
ENSG00000227268	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10509545	0.90[ASN][1000 genomes]
rs12411841	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12412766	0.90[ASN][1000 genomes]
rs12412793	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12414838	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12569919	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs12572530	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1342454	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17096268	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17109077	1.00[JPT][hapmap]
rs17111348	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1857157	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.90[ASN][1000 genomes]
rs4934405	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.90[ASN][1000 genomes]
rs4934412	1.00[CHB][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895879	chr10:90015725-90219298	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv482385	chr10:90066140-90259751	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv948664	chr10:90076715-90517150	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1054984	chr10:90122512-90278038	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1050587	chr10:90146582-90272627	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv540739	chr10:90146582-90272627	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90144600-90149000	Enhancers	Small Intestine	intestine
2	chr10:90144800-90149600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr10:90145800-90149200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr10:90146000-90149000	Enhancers	Fetal Heart	heart
5	chr10:90146200-90149000	Enhancers	Primary T cells fromperipheralblood	blood
6	chr10:90146200-90150000	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr10:90146200-90150200	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr10:90146400-90148800	Enhancers	Sigmoid Colon	Sigmoid Colon
9	chr10:90146400-90149800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr10:90146600-90149800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr10:90146800-90155200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr10:90147000-90148800	Enhancers	Duodenum Mucosa	Duodenum
13	chr10:90147000-90149200	Enhancers	Fetal Intestine Small	intestine
14	chr10:90147000-90149600	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr10:90147000-90149800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr10:90147000-90150000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr10:90147000-90150200	Enhancers	Stomach Mucosa	stomach
18	chr10:90147000-90150600	Enhancers	Primary B cells from peripheral blood	blood
19	chr10:90147000-90152400	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr10:90147200-90149000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr10:90147200-90149000	Enhancers	Fetal Intestine Large	intestine
22	chr10:90147200-90149400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr10:90147200-90149600	Enhancers	Adipose Nuclei	Adipose
24	chr10:90147200-90149800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr10:90147200-90150200	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr10:90147200-90150400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr10:90147200-90151600	Weak transcription	HMEC	breast
28	chr10:90147200-90152000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr10:90147200-90152400	Enhancers	Primary hematopoietic stem cells	blood
30	chr10:90147400-90149400	Enhancers	Fetal Kidney	kidney
31	chr10:90147400-90149400	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr10:90147400-90149800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr10:90147400-90150200	Enhancers	Liver	Liver
34	chr10:90147400-90151800	Enhancers	Primary T cells from cord blood	blood
35	chr10:90147400-90152000	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr10:90147400-90152600	Enhancers	Primary B cells from cord blood	blood
37	chr10:90147600-90148800	Enhancers	Pancreatic Islets	Pancreatic Islet
38	chr10:90147600-90149000	Weak transcription	NHLF	lung
39	chr10:90147600-90149200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr10:90147600-90150400	Enhancers	Thymus	Thymus
41	chr10:90147600-90151800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr10:90147600-90152000	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr10:90147600-90152800	Enhancers	Fetal Thymus	thymus
44	chr10:90147800-90148800	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr10:90147800-90148800	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr10:90147800-90149800	Weak transcription	Fetal Lung	lung
47	chr10:90147800-90151400	Enhancers	GM12878-XiMat	blood
48	chr10:90147800-90154600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr10:90148200-90149600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr10:90148200-90149600	Weak transcription	Skeletal Muscle Female	skeletal muscle

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