Variant report

Variant	rs6518204
Chromosome Location	chr21:46187385-46187386
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:46183165..46184854-chr21:46185530..46187850,2	K562	blood:
2	chr21:46021562..46023632-chr21:46186668..46188181,2	K562	blood:
3	chr21:46185007..46187777-chr21:46197158..46201208,5	MCF-7	breast:
4	chr21:46184586..46187452-chr21:46187793..46189728,3	MCF-7	breast:
5	chr21:46181841..46189587-chr21:46189919..46197097,16	MCF-7	breast:
6	chr21:46171917..46177806-chr21:46181342..46188371,13	MCF-7	breast:
7	chr21:46187285..46189608-chr21:46193802..46195925,2	K562	blood:
8	chr21:46186765..46188429-chr21:46235591..46237706,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000184787	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1071792	0.88[ASN][1000 genomes]
rs11088963	0.97[ASN][1000 genomes]
rs1109280	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11701732	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11702064	0.91[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11702743	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13049657	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13050872	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1821431	1.00[ASN][1000 genomes]
rs2294157	1.00[ASN][1000 genomes]
rs2329900	0.80[GIH][hapmap]
rs2838674	0.80[EUR][1000 genomes]
rs2838675	0.85[CHD][hapmap]
rs2838678	1.00[ASN][1000 genomes]
rs2838686	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2838699	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35209090	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35242981	0.88[ASN][1000 genomes]
rs35933313	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3788136	0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs4239838	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4818734	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4818975	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs62220109	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62222752	0.92[ASN][1000 genomes]
rs71322592	0.86[EUR][1000 genomes]
rs7281735	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs760430	0.85[CHD][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs760431	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs760432	0.88[ASN][1000 genomes]
rs8103	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs876812	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs885655	0.85[CHD][hapmap]
rs885657	0.85[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916258	chr21:45995986-46624705	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
2	nsv913956	chr21:46096964-46279505	Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv1062245	chr21:46096964-46332587	Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv544478	chr21:46096964-46332587	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6518204	PCBP3	cis	parietal	SCAN
rs6518204	PTTG1IP	cis	parietal	SCAN
rs6518204	UBE2G2	cis	parietal	SCAN
rs6518204	PDE1B	trans	cerebellum	SCAN
rs6518204	NCRNA00175	cis	parietal	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46181200-46188000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr21:46181800-46188000	Weak transcription	Fetal Intestine Small	intestine
3	chr21:46181800-46188400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr21:46182200-46189000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr21:46182600-46188600	Weak transcription	Liver	Liver
6	chr21:46183600-46190800	Weak transcription	A549	lung
7	chr21:46184400-46187400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr21:46184600-46187600	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr21:46184600-46189000	Enhancers	H1 Cell Line	embryonic stem cell
10	chr21:46184600-46189200	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr21:46184800-46188000	Weak transcription	Lung	lung
12	chr21:46184800-46188600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr21:46184800-46188800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr21:46184800-46188800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr21:46184800-46189600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr21:46185000-46188000	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr21:46185000-46188200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr21:46185200-46188000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr21:46185200-46188000	Weak transcription	Brain Germinal Matrix	brain
20	chr21:46185200-46189000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
21	chr21:46185200-46189600	Weak transcription	NHLF	lung
22	chr21:46185600-46187400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr21:46185600-46187400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr21:46185600-46188000	Weak transcription	Duodenum Mucosa	Duodenum
25	chr21:46185600-46188200	Weak transcription	Primary T cells from cord blood	blood
26	chr21:46185600-46188200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr21:46185600-46190800	Weak transcription	Brain Anterior Caudate	brain
28	chr21:46185600-46190800	Weak transcription	Hela-S3	cervix
29	chr21:46185800-46187400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr21:46185800-46187600	Weak transcription	Thymus	Thymus
31	chr21:46185800-46188000	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr21:46185800-46188000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr21:46185800-46188000	Weak transcription	Fetal Brain Female	brain
34	chr21:46185800-46188400	Weak transcription	Adipose Nuclei	Adipose
35	chr21:46185800-46188400	Weak transcription	Ovary	ovary
36	chr21:46185800-46189600	Weak transcription	Fetal Intestine Large	intestine
37	chr21:46185800-46192600	Weak transcription	Primary hematopoietic stem cells	blood
38	chr21:46185800-46199600	Weak transcription	Stomach Mucosa	stomach
39	chr21:46186000-46187600	Weak transcription	Fetal Heart	heart
40	chr21:46186000-46188200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr21:46186000-46189600	Weak transcription	Primary B cells from peripheral blood	blood
42	chr21:46186000-46189600	Weak transcription	Fetal Lung	lung
43	chr21:46186000-46189600	Weak transcription	Left Ventricle	heart
44	chr21:46186000-46189800	Weak transcription	HSMMtube	muscle
45	chr21:46186000-46190600	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr21:46186000-46190800	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr21:46186200-46187400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr21:46186200-46187400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr21:46186200-46187400	Enhancers	HMEC	breast
50	chr21:46186200-46187800	Weak transcription	Right Ventricle	heart

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