Variant report

Variant	rs9462553
Chromosome Location	chr6:39463562-39463563
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	chr6:39463170..39464911-chr6:39479174..39481419,2	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs11961693	0.82[ASN][1000 genomes]
rs11962587	0.83[CHB][hapmap]
rs11964924	0.84[CHB][hapmap]
rs11968704	0.94[CHB][hapmap];0.83[ASN][1000 genomes]
rs11969059	0.89[CHB][hapmap]
rs12664369	0.83[CHB][hapmap]
rs1546910	0.85[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs16892158	0.83[CHB][hapmap]
rs17457401	0.85[ASN][1000 genomes]
rs2026670	0.83[JPT][hapmap]
rs2038198	0.83[CHB][hapmap]
rs2073134	0.85[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs2235817	0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs2273063	0.94[CHB][hapmap];0.80[CHD][hapmap]
rs3736735	0.83[CHB][hapmap]
rs4236064	0.83[CHB][hapmap];0.80[CHD][hapmap];0.88[JPT][hapmap]
rs4446568	0.82[ASN][1000 genomes]
rs4482968	0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs4482969	0.82[ASN][1000 genomes]
rs4540261	0.94[CHB][hapmap]
rs4714255	0.83[CHB][hapmap]
rs4714256	0.89[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs58087685	0.85[ASN][1000 genomes]
rs6930913	0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs9296298	0.83[JPT][hapmap]
rs9296299	0.83[CHB][hapmap]
rs9296300	0.83[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.92[ASN][1000 genomes]
rs9357306	0.87[ASN][1000 genomes]
rs9357307	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9357308	0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs9357309	0.94[CHB][hapmap];0.81[ASN][1000 genomes]
rs9367008	0.89[CHB][hapmap]
rs9367009	0.89[CHB][hapmap]
rs9367012	0.94[CHB][hapmap];0.83[ASN][1000 genomes]
rs9367014	0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs9367015	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9367016	0.82[ASN][1000 genomes]
rs9367017	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9369119	0.94[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap]
rs9380867	0.84[CHB][hapmap]
rs9380868	0.87[CHB][hapmap]
rs9380871	0.82[ASN][1000 genomes]
rs9380872	0.82[ASN][1000 genomes]
rs9380873	0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs9380874	0.84[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs9380877	0.83[CHB][hapmap]
rs9380880	0.83[CHB][hapmap]
rs9394598	0.84[CHB][hapmap]
rs9394599	0.89[CHB][hapmap]
rs9394600	0.83[CHB][hapmap]
rs9394602	0.94[CHB][hapmap];0.81[ASN][1000 genomes]
rs9394603	0.81[ASN][1000 genomes]
rs9394606	0.94[CHB][hapmap]
rs9394608	0.83[CHB][hapmap]
rs9394609	0.83[CHB][hapmap]
rs9394611	0.83[CHB][hapmap]
rs9394614	0.83[CHB][hapmap]
rs9471113	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs9471117	0.85[YRI][hapmap]
rs9471118	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[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	nsv885822	chr6:39327708-39721216	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv885823	chr6:39421715-39526867	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9462553	CCND3	cis	cerebellum	SCAN
rs9462553	RRP36	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39455400-39465200	Weak transcription	Right Atrium	heart
2	chr6:39456800-39468400	Weak transcription	Brain Hippocampus Middle	brain
3	chr6:39461600-39464200	Weak transcription	Adipose Nuclei	Adipose
4	chr6:39461600-39464600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr6:39461600-39464800	Weak transcription	NHDF-Ad	bronchial
6	chr6:39461800-39463600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr6:39461800-39464800	Weak transcription	Placenta	Placenta
8	chr6:39461800-39465200	Weak transcription	Fetal Kidney	kidney
9	chr6:39462000-39464400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr6:39462000-39465000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr6:39462200-39463800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr6:39462600-39464200	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr6:39462600-39464400	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr6:39462600-39464400	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr6:39462600-39464400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr6:39462600-39466200	Enhancers	Fetal Lung	lung
17	chr6:39462800-39464200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
18	chr6:39462800-39464200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr6:39462800-39464400	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr6:39462800-39464400	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr6:39462800-39465000	Enhancers	H1 Cell Line	embryonic stem cell
22	chr6:39462800-39465000	Enhancers	H9 Cell Line	embryonic stem cell
23	chr6:39462800-39467000	Enhancers	Fetal Stomach	stomach
24	chr6:39463000-39466400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr6:39463200-39464000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr6:39463200-39464400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr6:39463400-39463600	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr6:39463400-39463800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell

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