Variant report

Variant	rs954466
Chromosome Location	chr6:150949327-150949328
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	chr6:150944124..150946424-chr6:150947908..150950533,2	MCF-7	breast:
2	chr6:150947452..150949419-chr6:150952657..150955576,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000224029	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12527099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2101665	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4870536	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.88[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57241701	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62432655	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9371465	0.95[EUR][1000 genomes]
rs9398028	1.00[CEU][hapmap];1.00[TSI][hapmap];0.97[EUR][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	nsv886772	chr6:150743364-151024280	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv886774	chr6:150931131-150983318	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv522403	chr6:150947524-150950215	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs954466	C6orf97	cis	cerebellum	SCAN
rs954466	STXBP5	cis	cerebellum	SCAN
rs954466	ZC3H12D	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150928400-150952800	Weak transcription	Right Ventricle	heart
2	chr6:150939000-150949600	Weak transcription	Pancreas	Pancrea
3	chr6:150939000-150954200	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr6:150941200-150953000	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr6:150941800-150954000	Weak transcription	Brain Angular Gyrus	brain
6	chr6:150941800-150962600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr6:150942000-150949600	Weak transcription	Colonic Mucosa	Colon
8	chr6:150942000-150949600	Weak transcription	Gastric	stomach
9	chr6:150945000-150950000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr6:150945000-150954200	Weak transcription	Aorta	Aorta
11	chr6:150945600-150950000	Weak transcription	Lung	lung
12	chr6:150947200-150953400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr6:150947400-150949600	Enhancers	Primary hematopoietic stem cells	blood
14	chr6:150947400-150950400	Enhancers	Fetal Intestine Large	intestine
15	chr6:150947400-150950400	Enhancers	Fetal Kidney	kidney
16	chr6:150947400-150950400	Enhancers	Fetal Lung	lung
17	chr6:150947400-150950400	Enhancers	Fetal Stomach	stomach
18	chr6:150947400-150950400	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr6:150947400-150950400	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr6:150947600-150949600	Enhancers	Adipose Nuclei	Adipose
21	chr6:150947600-150950400	Enhancers	Rectal Mucosa Donor 29	rectum
22	chr6:150947600-150951800	Enhancers	HepG2	liver
23	chr6:150947600-150952800	Enhancers	Duodenum Mucosa	Duodenum
24	chr6:150947600-150957400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr6:150947800-150949600	Weak transcription	Left Ventricle	heart
26	chr6:150947800-150950200	Enhancers	Fetal Brain Male	brain
27	chr6:150947800-150951800	Weak transcription	Placenta	Placenta
28	chr6:150947800-150959400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:150948000-150949400	Enhancers	Liver	Liver
30	chr6:150948000-150949600	Weak transcription	Right Atrium	heart
31	chr6:150948000-150949600	Weak transcription	Spleen	Spleen
32	chr6:150948000-150950000	Enhancers	HUVEC	blood vessel
33	chr6:150948000-150953800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr6:150948200-150949600	Enhancers	Primary B cells from peripheral blood	blood
35	chr6:150948200-150950000	Enhancers	Fetal Thymus	thymus
36	chr6:150948200-150950000	Enhancers	Thymus	Thymus
37	chr6:150948200-150952400	Weak transcription	Fetal Muscle Trunk	muscle
38	chr6:150948400-150949400	Enhancers	Primary T cells from cord blood	blood
39	chr6:150948400-150950000	Enhancers	Fetal Brain Female	brain
40	chr6:150948600-150950800	Enhancers	Fetal Intestine Small	intestine
41	chr6:150948800-150949400	Enhancers	NH-A	brain
42	chr6:150948800-150949600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr6:150948800-150950200	Enhancers	Fetal Heart	heart
44	chr6:150948800-150950200	Enhancers	Rectal Smooth Muscle	rectum
45	chr6:150948800-150950400	Enhancers	Stomach Mucosa	stomach
46	chr6:150949000-150950400	Enhancers	Fetal Muscle Leg	muscle
47	chr6:150949000-150950400	Enhancers	Small Intestine	intestine
48	chr6:150949000-150958000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr6:150949200-150952600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr6:150949200-150952600	Weak transcription	Duodenum Smooth Muscle	Duodenum

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