Variant report

Variant	rs12664861
Chromosome Location	chr6:167033955-167033956
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:167027450..167030161-chr6:167032275..167034525,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10223606	1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12333057	0.81[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12663354	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12664453	0.81[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12664885	0.97[ASN][1000 genomes]
rs3778374	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3778376	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3799569	0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6909203	0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6932695	0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs763191	0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7760180	0.81[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9457191	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9459702	1.00[ASW][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9459704	0.81[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9459705	0.81[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9459707	0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3490076	chr6:166727901-167306743	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
2	esv3490077	chr6:166727901-167306743	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
3	nsv605260	chr6:166984094-167455139	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
4	nsv432984	chr6:167018915-167181613	Bivalent Enhancer Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1023649	chr6:167026469-167060732	Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:167012400-167034400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:167016000-167034400	Weak transcription	Aorta	Aorta
3	chr6:167025400-167034800	Enhancers	Ovary	ovary
4	chr6:167025600-167034200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr6:167028200-167035400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr6:167028600-167034600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr6:167029200-167034400	Weak transcription	Colonic Mucosa	Colon
8	chr6:167029200-167039000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr6:167029400-167036800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:167029600-167034200	Weak transcription	Brain Substantia Nigra	brain
11	chr6:167031400-167034400	Weak transcription	Fetal Kidney	kidney
12	chr6:167031600-167037200	Enhancers	Placenta Amnion	Placenta Amnion
13	chr6:167032200-167034600	Enhancers	HSMMtube	muscle
14	chr6:167032200-167034800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr6:167032200-167034800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr6:167032400-167034200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr6:167032400-167034400	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr6:167032400-167034400	Weak transcription	Spleen	Spleen
19	chr6:167032400-167035000	Enhancers	Fetal Heart	heart
20	chr6:167032600-167034200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr6:167032600-167034200	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr6:167032600-167034200	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr6:167032600-167034200	Weak transcription	Duodenum Mucosa	Duodenum
24	chr6:167032600-167034200	Weak transcription	Gastric	stomach
25	chr6:167032600-167034400	Enhancers	HSMM	muscle
26	chr6:167032600-167034600	Enhancers	Esophagus	oesophagus
27	chr6:167032600-167034600	Enhancers	Right Ventricle	heart
28	chr6:167032600-167035200	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr6:167032600-167035400	Enhancers	Fetal Muscle Leg	muscle
30	chr6:167032600-167035400	Enhancers	Left Ventricle	heart
31	chr6:167032600-167035400	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr6:167032600-167035600	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr6:167032600-167035600	Enhancers	Brain Germinal Matrix	brain
34	chr6:167032600-167038600	Enhancers	NHLF	lung
35	chr6:167032600-167039400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr6:167032800-167034000	Enhancers	Fetal Stomach	stomach
37	chr6:167032800-167034000	Enhancers	HMEC	breast
38	chr6:167032800-167034200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr6:167032800-167034400	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr6:167032800-167034800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr6:167032800-167034800	Enhancers	Colon Smooth Muscle	Colon
42	chr6:167032800-167034800	Enhancers	Rectal Smooth Muscle	rectum
43	chr6:167032800-167036600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr6:167032800-167039000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr6:167032800-167039000	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr6:167033000-167034200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr6:167033000-167034400	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr6:167033000-167034400	Enhancers	Lung	lung
49	chr6:167033000-167034400	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr6:167033000-167034600	Enhancers	Duodenum Smooth Muscle	Duodenum

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