Variant report

Variant	rs6488523
Chromosome Location	chr12:12584162-12584163
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:12583532..12588192-chr12:12712241..12716569,6	MCF-7	breast:
2	chr12:12582548..12584902-chr12:12602163..12604980,2	MCF-7	breast:
3	chr12:12583518..12585650-chr12:12588474..12590636,2	K562	blood:
4	chr12:12584022..12586208-chr12:12592875..12596434,3	MCF-7	breast:
5	chr12:12578734..12582406-chr12:12583548..12588483,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111266	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11831188	1.00[ASN][1000 genomes]
rs11831555	0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs16908006	0.89[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16908019	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1861674	0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2193270	0.93[YRI][hapmap];0.87[AFR][1000 genomes]
rs4763824	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4763827	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4763828	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4763831	0.83[ASN][1000 genomes]
rs56261569	0.81[ASN][1000 genomes]
rs58218344	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58529509	1.00[ASN][1000 genomes]
rs60022096	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60363317	1.00[ASN][1000 genomes]
rs60971404	1.00[ASN][1000 genomes]
rs6488521	1.00[ASN][1000 genomes]
rs6488524	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488527	1.00[CEU][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7133988	1.00[ASN][1000 genomes]
rs7134787	0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs714480	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7306292	0.90[YRI][hapmap];0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73287587	1.00[ASN][1000 genomes]
rs7957014	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973069	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7975061	0.96[YRI][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7978842	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7980390	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs888198	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS 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 miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv1812889	chr12:12510842-12593406	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12558000-12586000	Weak transcription	Pancreas	Pancrea
2	chr12:12565200-12585000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr12:12572600-12588400	Weak transcription	Primary T cells from cord blood	blood
4	chr12:12578200-12588600	Weak transcription	Primary B cells from cord blood	blood
5	chr12:12578400-12586600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:12578400-12588200	Weak transcription	Primary B cells from peripheral blood	blood
7	chr12:12578800-12586200	Weak transcription	Brain Hippocampus Middle	brain
8	chr12:12578800-12589200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr12:12579200-12585200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr12:12579400-12585000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr12:12579400-12587000	Weak transcription	Psoas Muscle	Psoas
12	chr12:12579600-12585200	Weak transcription	Stomach Mucosa	stomach
13	chr12:12579600-12586600	Weak transcription	Fetal Intestine Large	intestine
14	chr12:12580000-12588600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr12:12580600-12584400	Enhancers	HMEC	breast
16	chr12:12580800-12587400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr12:12581000-12586000	Weak transcription	Esophagus	oesophagus
18	chr12:12581200-12587000	Enhancers	NHEK	skin
19	chr12:12581600-12588800	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr12:12582000-12589200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr12:12582200-12584600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr12:12582400-12585200	Weak transcription	HepG2	liver
23	chr12:12582600-12584400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr12:12582600-12585400	Weak transcription	Aorta	Aorta
25	chr12:12582600-12585600	Weak transcription	Brain Angular Gyrus	brain
26	chr12:12582600-12586400	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr12:12582600-12592000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr12:12582600-12595000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr12:12582600-12599400	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr12:12582800-12586000	Weak transcription	Fetal Thymus	thymus
31	chr12:12582800-12592600	Weak transcription	NH-A	brain
32	chr12:12582800-12596400	Weak transcription	Spleen	Spleen
33	chr12:12583000-12585200	Weak transcription	Brain Cingulate Gyrus	brain
34	chr12:12583000-12586200	Weak transcription	Thymus	Thymus
35	chr12:12583000-12586600	Weak transcription	Placenta	Placenta
36	chr12:12583000-12588600	Weak transcription	GM12878-XiMat	blood
37	chr12:12583000-12589400	Weak transcription	HSMM	muscle
38	chr12:12583000-12594000	Weak transcription	HSMMtube	muscle
39	chr12:12583400-12585000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr12:12583400-12587400	Enhancers	NHLF	lung
41	chr12:12583600-12584200	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr12:12583600-12584200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr12:12583600-12584600	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr12:12583600-12584600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr12:12583600-12586000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr12:12583600-12588000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr12:12583800-12584200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr12:12583800-12584200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr12:12583800-12584200	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr12:12583800-12584200	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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