Variant report

Variant	rs9458252
Chromosome Location	chr6:161860169-161860170
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:161860070..161861572-chr6:161862140..161863792,2	MCF-7	breast:
2	chr6:161848154..161849846-chr6:161859403..161861110,2	MCF-7	breast:
3	chr6:161859122..161861758-chr6:161866811..161869668,2	MCF-7	breast:
4	chr6:161855024..161858360-chr6:161858723..161860898,4	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs10806745	0.96[CEU][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6921435	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3381361	chr6:161373617-161864101	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv481931	chr6:161647026-161961906	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv1031234	chr6:161676768-162250726	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv886819	chr6:161712035-162520133	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv886820	chr6:161712880-162184932	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv830854	chr6:161739926-161927515	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv518931	chr6:161793319-162406335	Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv481861	chr6:161802883-162160197	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv1024921	chr6:161814295-161860636	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	esv2761040	chr6:161814307-161860636	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv1018065	chr6:161816661-161860169	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv1018466	chr6:161816661-161860636	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv1023319	chr6:161817703-161860636	Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv481981	chr6:161829077-162215745	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv1015211	chr6:161836242-161860636	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv1033603	chr6:161844266-162001436	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	nsv481750	chr6:161850976-161996586	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9458252	SNORA29	cis	cerebellum	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:161855600-161864400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:161855800-161860200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:161856000-161861600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr6:161856200-161860200	Weak transcription	Left Ventricle	heart
5	chr6:161856400-161860200	Weak transcription	Ovary	ovary
6	chr6:161856600-161866200	Weak transcription	Psoas Muscle	Psoas
7	chr6:161856800-161860200	Weak transcription	Colon Smooth Muscle	Colon
8	chr6:161856800-161861400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr6:161857800-161863400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr6:161858400-161862800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:161859000-161860200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr6:161859400-161860200	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr6:161859400-161860600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:161859800-161860200	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr6:161859800-161860200	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr6:161859800-161860200	Flanking Active TSS	Brain Anterior Caudate	brain
17	chr6:161859800-161860200	Flanking Active TSS	Brain Germinal Matrix	brain
18	chr6:161859800-161860600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:161859800-161860600	Active TSS	Brain Substantia Nigra	brain
20	chr6:161859800-161860600	Flanking Active TSS	HSMMtube	muscle
21	chr6:161859800-161860600	Flanking Active TSS	NHDF-Ad	bronchial
22	chr6:161859800-161860800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
23	chr6:161859800-161860800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr6:161859800-161860800	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr6:161860000-161860200	Flanking Active TSS	Fetal Brain Male	brain
26	chr6:161860000-161860200	Active TSS	Skeletal Muscle Male	skeletal muscle
27	chr6:161860000-161860200	Flanking Active TSS	NH-A	brain
28	chr6:161860000-161860200	Flanking Active TSS	Osteobl	bone
29	chr6:161860000-161860400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr6:161860000-161860400	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr6:161860000-161860400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr6:161860000-161860400	Active TSS	Pancreas	Pancrea
33	chr6:161860000-161860400	Active TSS	Stomach Smooth Muscle	stomach
34	chr6:161860000-161860400	Flanking Active TSS	HSMM	muscle
35	chr6:161860000-161860600	Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr6:161860000-161860600	Active TSS	Brain Angular Gyrus	brain
37	chr6:161860000-161860600	Active TSS	Brain Hippocampus Middle	brain
38	chr6:161860000-161860600	Active TSS	Brain Inferior Temporal Lobe	brain
39	chr6:161860000-161860600	Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr6:161860000-161860600	Flanking Active TSS	Fetal Kidney	kidney
41	chr6:161860000-161860600	Enhancers	Fetal Muscle Trunk	muscle
42	chr6:161860000-161860600	Active TSS	Rectal Mucosa Donor 29	rectum
43	chr6:161860000-161860600	Active TSS	Rectal Smooth Muscle	rectum
44	chr6:161860000-161860600	Active TSS	Right Atrium	heart
45	chr6:161860000-161860600	Active TSS	A549	lung
46	chr6:161860000-161860600	Flanking Active TSS	HMEC	breast
47	chr6:161860000-161860600	Enhancers	HUVEC	blood vessel
48	chr6:161860000-161860800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr6:161860000-161860800	Active TSS	Adipose Nuclei	Adipose
50	chr6:161860000-161860800	Active TSS	Brain Cingulate Gyrus	brain

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