Variant report

Variant	rs2837220
Chromosome Location	chr21:41160938-41160939
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr21:41160202-41161016	ECC-1	luminal epithelium:	n/a	chr21:41160437-41160453
2	SIN3AK20	chr21:41160045-41160944	MCF-7	breast:	n/a	n/a
3	NFIC	chr21:41160122-41160947	ECC-1	luminal epithelium:	n/a	n/a
4	TCF12	chr21:41160211-41161012	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:41160210..41160951-chr21:41226545..41227182,3	MCF-7	breast:
2	chr21:41159565..41161270-chr21:41282682..41284025,38	MCF-7	breast:
3	chr21:41160014..41161121-chr21:41238636..41239761,13	MCF-7	breast:
4	chr21:41159877..41161605-chr21:41224829..41226757,2	MCF-7	breast:
5	chr21:41159946..41160938-chr21:41279878..41281257,7	MCF-7	breast:
6	chr21:41159912..41160982-chr21:41296603..41297482,6	MCF-7	breast:
7	chr21:41160053..41161081-chr21:41282734..41283845,12	MCF-7	breast:

No data

Variant related genes	Relation type
IGSF5	TF binding region
ENSG00000183036	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1018350	0.85[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs1018351	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs11088495	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1118102	0.83[ASN][1000 genomes]
rs1118103	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs1571713	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs2142194	0.83[ASN][1000 genomes]
rs2178882	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs2837209	0.83[ASN][1000 genomes]
rs2837211	0.85[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs2837212	0.85[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs2837216	0.85[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs2837224	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs455830	0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs455942	0.83[ASN][1000 genomes]
rs456522	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs456818	0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs457569	0.89[JPT][hapmap]
rs458406	0.85[CHD][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs460549	0.85[CHD][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs462163	0.86[ASN][1000 genomes]
rs462555	0.85[CHD][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs463903	0.85[CHD][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs464201	0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs464351	0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs464574	0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs464623	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs465258	0.87[CHD][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs466303	0.85[CHD][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs467044	0.83[ASN][1000 genomes]
rs4816657	0.85[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs4816658	0.85[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs4818091	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs4818096	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs760285	0.85[MKK][hapmap]
rs9983185	0.88[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061454	chr21:40757973-41265404	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1057956	chr21:40907707-41393396	Enhancers Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS 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	15 gene(s)	inside rSNPs	diseases
3	nsv544444	chr21:40907707-41393396	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1065086	chr21:41034806-41429078	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv544445	chr21:41034806-41429078	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv834099	chr21:41076873-41206030	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv3329011	chr21:41158272-41160991	Active TSS Enhancers Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2837220	FSCN1	trans	parietal	SCAN
rs2837220	MORC3	cis	cerebellum	SCAN
rs2837220	MORC3	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:41160000-41163600	Enhancers	Fetal Heart	heart
2	chr21:41160200-41161400	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr21:41160400-41161000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr21:41160400-41161000	Flanking Active TSS	Fetal Kidney	kidney
5	chr21:41160400-41161000	Enhancers	Fetal Muscle Leg	muscle
6	chr21:41160400-41161200	Active TSS	Right Ventricle	heart
7	chr21:41160400-41161400	Enhancers	Placenta	Placenta
8	chr21:41160600-41161000	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr21:41160600-41161000	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr21:41160600-41161000	Enhancers	Fetal Lung	lung
11	chr21:41160600-41161200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr21:41160600-41161200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr21:41160600-41161200	Enhancers	Fetal Stomach	stomach
14	chr21:41160600-41161200	Active TSS	Left Ventricle	heart
15	chr21:41160600-41161400	Enhancers	Pancreas	Pancrea
16	chr21:41160600-41161400	Active TSS	Right Atrium	heart
17	chr21:41160600-41163200	Weak transcription	Colon Smooth Muscle	Colon
18	chr21:41160800-41161000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr21:41160800-41161000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr21:41160800-41161200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr21:41160800-41161200	Enhancers	Placenta Amnion	Placenta Amnion
22	chr21:41160800-41161200	Enhancers	NH-A	brain
23	chr21:41160800-41161400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr21:41160800-41162000	Weak transcription	Fetal Brain Female	brain
25	chr21:41160800-41163000	Weak transcription	Rectal Smooth Muscle	rectum

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