Variant report

Variant	rs6516735
Chromosome Location	chr21:27861792-27861793
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	chr21:27541635..27543778-chr21:27861524..27863454,2	MCF-7	breast:
2	chr21:27861488..27864858-chr21:27865688..27868748,3	K562	blood:

Variant related genes	Relation type
ENSG00000142192	Chromatin interaction
ENSG00000273492	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs12483136	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1369171	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1478096	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs150753	0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1564167	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs170178	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs170179	0.85[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs178422	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs188816	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs219617	1.00[ASW][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.89[LWK][hapmap];0.94[MKK][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs219623	0.87[JPT][hapmap];0.84[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs219624	0.80[CHB][hapmap];0.87[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs219626	0.90[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs219627	0.85[CHB][hapmap];0.87[JPT][hapmap];0.95[ASN][1000 genomes]
rs219628	0.85[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs219629	0.85[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs219630	1.00[ASW][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];0.96[MKK][hapmap];0.82[TSI][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs219631	0.90[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs219633	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs219634	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs219635	0.90[CHB][hapmap];0.81[JPT][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2830249	0.81[CHB][hapmap]
rs36003638	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs456751	0.89[ASN][1000 genomes]
rs4817119	1.00[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.94[LWK][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs714428	0.90[CHB][hapmap];0.81[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs8128305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs979343	0.89[CHB][hapmap];0.80[CHD][hapmap]
rs9978642	0.86[YRI][hapmap]
rs9983959	0.81[AFR][1000 genomes]
rs9984299	0.86[LWK][hapmap];0.85[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1056506	chr21:27332898-28049880	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv544412	chr21:27332898-28049880	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv587335	chr21:27715263-27955385	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv913660	chr21:27815652-27869676	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv587336	chr21:27849346-27865978	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
6	esv1844181	chr21:27854701-27879342	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6516735	CCND3	trans	lymphoblastoid	seeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:27842400-27862000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr21:27843400-27878800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr21:27847000-27862800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr21:27849400-27863000	Weak transcription	Fetal Kidney	kidney
5	chr21:27851400-27863000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr21:27851400-27864000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr21:27852200-27863000	Weak transcription	Fetal Lung	lung
8	chr21:27852600-27862800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr21:27852600-27863000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr21:27852600-27867600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr21:27852800-27862000	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr21:27852800-27862200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr21:27852800-27871400	Weak transcription	Primary hematopoietic stem cells	blood
14	chr21:27853000-27863200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr21:27856600-27862800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr21:27859600-27862400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr21:27859600-27862400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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