Variant report

Variant	rs12527593
Chromosome Location	chr6:13419289-13419290
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:13417839..13420815-chr6:13486813..13488730,2	MCF-7	breast:
2	chr6:13417373..13420298-chr6:13574517..13576423,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000124523	Chromatin interaction
ENSG00000145990	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs12528480	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16874132	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16874136	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16874138	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16874139	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16874142	1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs16874145	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16874149	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16874152	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs16874153	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16874155	1.00[CHB][hapmap]
rs1992387	1.00[CHB][hapmap]
rs511996	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs56676493	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61017983	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6910199	0.83[EUR][1000 genomes]
rs6914294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6926083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6931031	1.00[CHB][hapmap]
rs6936420	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs73366922	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73366931	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73366933	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73366936	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73366937	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73366941	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73366945	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73366948	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73366949	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73366951	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73366952	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73366960	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73366970	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73725822	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7739372	1.00[CHB][hapmap]
rs7740220	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7740298	1.00[CHB][hapmap]
rs7746830	0.88[EUR][1000 genomes]
rs7750943	0.88[EUR][1000 genomes]
rs7758003	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9370100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13405000-13421800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:13408600-13422600	Weak transcription	HSMM	muscle
3	chr6:13408800-13419400	Weak transcription	Primary B cells from cord blood	blood
4	chr6:13408800-13420200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:13408800-13423000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:13411400-13419600	Weak transcription	Fetal Thymus	thymus
7	chr6:13411400-13421800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:13411600-13424200	Enhancers	Right Ventricle	heart
9	chr6:13413600-13419400	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr6:13413600-13419800	Weak transcription	Esophagus	oesophagus
11	chr6:13413800-13419600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr6:13414000-13420000	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr6:13414000-13421400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:13414000-13421800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr6:13414000-13421800	Weak transcription	Brain Germinal Matrix	brain
16	chr6:13414000-13422000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr6:13414600-13422000	Weak transcription	NHLF	lung
18	chr6:13414800-13420200	Weak transcription	HSMMtube	muscle
19	chr6:13415000-13420000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr6:13415000-13420400	Weak transcription	Colon Smooth Muscle	Colon
21	chr6:13415200-13419400	Enhancers	Stomach Smooth Muscle	stomach
22	chr6:13415200-13419600	Weak transcription	Primary T cells from cord blood	blood
23	chr6:13415200-13420200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr6:13415400-13419400	Weak transcription	Fetal Lung	lung
25	chr6:13415400-13422600	Weak transcription	Gastric	stomach
26	chr6:13417200-13420400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr6:13417200-13424200	Enhancers	Brain Angular Gyrus	brain
28	chr6:13417400-13419600	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr6:13417600-13422000	Enhancers	Brain Hippocampus Middle	brain
30	chr6:13417600-13424000	Enhancers	Brain Cingulate Gyrus	brain
31	chr6:13417800-13420400	Enhancers	Pancreas	Pancrea
32	chr6:13417800-13420800	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr6:13417800-13424000	Enhancers	Adipose Nuclei	Adipose
34	chr6:13417800-13424200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr6:13417800-13424200	Enhancers	Left Ventricle	heart
36	chr6:13417800-13424600	Enhancers	Right Atrium	heart
37	chr6:13417800-13424800	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr6:13417800-13427000	Enhancers	Psoas Muscle	Psoas
39	chr6:13418200-13419600	Strong transcription	GM12878-XiMat	blood
40	chr6:13418200-13420600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr6:13418200-13421400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr6:13418200-13421600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr6:13418200-13421800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr6:13418400-13419600	Weak transcription	Lung	lung
45	chr6:13418400-13420200	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr6:13418400-13421000	Enhancers	Liver	Liver
47	chr6:13418400-13421400	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr6:13418400-13421800	Weak transcription	Fetal Kidney	kidney
49	chr6:13418600-13419800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr6:13418600-13420000	Enhancers	ES-I3 Cell Line	embryonic stem cell

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