Variant report

Variant	rs11171671
Chromosome Location	chr12:56154851-56154852
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:56136172..56137723-chr12:56154043..56156906,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135414	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10082864	0.82[ASN][1000 genomes]
rs10083186	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10161417	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11171667	0.85[AFR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11171670	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171677	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11171681	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11829536	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11834264	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12304296	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12304507	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12320756	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17117974	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3759101	0.82[ASN][1000 genomes]
rs7297523	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7299222	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7971247	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7972345	0.81[ASN][1000 genomes]
rs868051	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9739244	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832423	chr12:56080822-56253698	Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv469410	chr12:56098038-56170893	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
3	nsv559004	chr12:56098038-56170893	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56139400-56174600	Weak transcription	Stomach Mucosa	stomach
2	chr12:56141600-56161400	Strong transcription	Primary T cells from cord blood	blood
3	chr12:56141800-56157600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr12:56141800-56158000	Strong transcription	Fetal Intestine Large	intestine
5	chr12:56142000-56191800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr12:56142200-56161000	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr12:56142200-56162000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr12:56142400-56155400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr12:56142400-56155800	Strong transcription	NHLF	lung
10	chr12:56142400-56157400	Strong transcription	Thymus	Thymus
11	chr12:56142400-56161400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr12:56142600-56157600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr12:56142600-56157600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr12:56142600-56158000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr12:56142600-56161000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr12:56142600-56161200	Strong transcription	Dnd41	blood
17	chr12:56142600-56162000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr12:56142800-56158200	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr12:56143000-56158200	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr12:56143200-56158600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr12:56143200-56161400	Strong transcription	Fetal Muscle Leg	muscle
22	chr12:56143400-56158000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr12:56143800-56158200	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr12:56143800-56170000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr12:56144000-56156000	Strong transcription	Primary hematopoietic stem cells	blood
26	chr12:56144400-56155400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr12:56144400-56156600	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr12:56144600-56155400	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr12:56144600-56155800	Strong transcription	Duodenum Mucosa	Duodenum
30	chr12:56144600-56158000	Strong transcription	HSMM	muscle
31	chr12:56144600-56208800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr12:56144800-56157000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr12:56144800-56157800	Strong transcription	HepG2	liver
34	chr12:56144800-56158000	Strong transcription	Liver	Liver
35	chr12:56144800-56161200	Strong transcription	Fetal Thymus	thymus
36	chr12:56144800-56198600	Strong transcription	Primary B cells from peripheral blood	blood
37	chr12:56145000-56155600	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr12:56145000-56156200	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr12:56145000-56156800	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr12:56145000-56157200	Strong transcription	NH-A	brain
41	chr12:56145000-56157600	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr12:56145000-56157800	Strong transcription	Adipose Nuclei	Adipose
43	chr12:56145000-56158200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr12:56145200-56160400	Strong transcription	A549	lung
45	chr12:56145200-56199400	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr12:56145400-56156800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr12:56145400-56157600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr12:56146600-56161400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr12:56146600-56166200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr12:56146800-56157400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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