Variant report

Variant	rs12627203
Chromosome Location	chr21:44815113-44815114
allele	C/T
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:44815060..44818053-chr21:44827899..44829488,2	MCF-7	breast:
2	chr21:44769641..44773201-chr21:44814648..44818595,3	MCF-7	breast:
3	chr21:44763173..44768518-chr21:44813268..44818095,5	MCF-7	breast:
4	chr21:44815027..44818660-chr21:44844165..44848384,7	MCF-7	breast:
5	chr21:44814074..44816129-chr21:44848271..44850690,2	K562	blood:
6	chr21:44814631..44820586-chr21:44845176..44849099,6	K562	blood:
7	chr21:44801294..44803832-chr21:44814842..44816860,2	MCF-7	breast:
8	chr21:44814731..44816926-chr21:44832531..44834607,2	MCF-7	breast:
9	chr21:44779798..44782094-chr21:44814719..44816894,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000142178	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11910909	0.94[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2838293	0.86[CHB][hapmap]
rs2838295	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs67059973	0.80[AMR][1000 genomes]
rs67784679	0.83[ASN][1000 genomes]
rs7281209	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1056684	chr21:44539714-44886119	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv913831	chr21:44563995-44931821	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
3	esv1817359	chr21:44699077-44821595	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1057726	chr21:44711850-44957303	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
5	nsv544466	chr21:44711850-44957303	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
6	nsv1058308	chr21:44722915-44825108	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv1063186	chr21:44729904-44828476	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv544467	chr21:44729904-44828476	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv913837	chr21:44731138-44853859	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
10	nsv913838	chr21:44740134-44931821	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
11	nsv913839	chr21:44750200-44931821	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
12	nsv913840	chr21:44750643-44823479	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
13	nsv913841	chr21:44761874-44853859	Bivalent/Poised TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
14	nsv913844	chr21:44779680-44875495	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
15	nsv913845	chr21:44781356-44874702	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
16	nsv470901	chr21:44781356-44884252	Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
17	nsv913846	chr21:44792003-44824854	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
18	nsv913847	chr21:44792003-44931821	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12627203	PCP4	cis	parietal	SCAN
rs12627203	PSMG1	cis	cerebellum	SCAN
rs12627203	KRTAP10-10	cis	cerebellum	SCAN
rs12627203	NCRNA00257	cis	parietal	SCAN
rs12627203	LOC284837	cis	parietal	SCAN
rs12627203	DSCAM	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:44790600-44830800	Weak transcription	Right Atrium	heart
2	chr21:44804400-44819000	Weak transcription	Gastric	stomach
3	chr21:44808400-44816600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr21:44808600-44823000	Weak transcription	Brain Germinal Matrix	brain
5	chr21:44811400-44815200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr21:44811800-44815200	Weak transcription	A549	lung
7	chr21:44814000-44817600	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr21:44814000-44819200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr21:44814000-44822400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr21:44814200-44815200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr21:44814200-44815600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr21:44814200-44817800	Enhancers	Placenta Amnion	Placenta Amnion
13	chr21:44814400-44815200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr21:44814400-44815200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr21:44814400-44815400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr21:44814400-44818200	Enhancers	Fetal Muscle Trunk	muscle
17	chr21:44814400-44822000	Enhancers	Placenta	Placenta
18	chr21:44814600-44815400	Weak transcription	Esophagus	oesophagus
19	chr21:44814600-44815600	Enhancers	Spleen	Spleen
20	chr21:44814600-44816400	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr21:44814800-44815200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
22	chr21:44814800-44815200	Enhancers	Hela-S3	cervix
23	chr21:44814800-44815400	Enhancers	H1 Cell Line	embryonic stem cell
24	chr21:44814800-44815600	Weak transcription	Primary B cells from peripheral blood	blood
25	chr21:44814800-44815600	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr21:44814800-44815800	Enhancers	HepG2	liver
27	chr21:44814800-44816600	Weak transcription	Primary B cells from cord blood	blood
28	chr21:44814800-44818000	Weak transcription	Fetal Lung	lung
29	chr21:44814800-44818200	Weak transcription	Fetal Kidney	kidney
30	chr21:44814800-44822200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr21:44815000-44818400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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