Variant report

Variant	rs3820455
Chromosome Location	chr1:220291487-220291488
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr1:220291339-220293017	K562	blood:	n/a	n/a
2	KAP1	chr1:220291246-220291564	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:220266254..220269129-chr1:220290209..220292443,2	MCF-7	breast:
2	chr1:220285273..220288143-chr1:220290128..220292284,2	K562	blood:

Variant related genes	Relation type
MIR215	TF binding region
ENSG00000067704	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10127631	0.87[GIH][hapmap]
rs1039206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10863539	0.87[GIH][hapmap]
rs11118501	0.87[GIH][hapmap]
rs1124763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12031256	0.90[EUR][1000 genomes]
rs12032738	1.00[YRI][hapmap]
rs12037712	0.87[GIH][hapmap];0.88[LWK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs12045447	0.83[AFR][1000 genomes]
rs12086760	0.87[GIH][hapmap]
rs1557130	1.00[CEU][hapmap]
rs17007107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17007135	0.85[MKK][hapmap];0.83[YRI][hapmap]
rs17007139	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34406824	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs3767656	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs41274792	0.86[ASN][1000 genomes]
rs57463200	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs58256586	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58966246	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59935950	0.81[AFR][1000 genomes]
rs60736051	0.85[AFR][1000 genomes]
rs73096563	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs73096575	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73096577	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73096595	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73098512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73098518	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73098527	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73098528	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73098530	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73098537	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73098550	0.83[AFR][1000 genomes]
rs73098551	0.83[AFR][1000 genomes]
rs73098553	0.83[AFR][1000 genomes]
rs73098579	0.81[AFR][1000 genomes]
rs874331	1.00[YRI][hapmap];0.83[AFR][1000 genomes]

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	nsv427930	chr1:220120379-220333434	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	744 gene(s)	inside rSNPs	diseases
2	nsv832636	chr1:220139697-220294352	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	738 gene(s)	inside rSNPs	diseases
3	esv2753619	chr1:220210273-220302117	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	737 gene(s)	inside rSNPs	diseases
4	nsv947468	chr1:220287976-220292749	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA	723 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220268400-220293400	Weak transcription	Stomach Mucosa	stomach
2	chr1:220268400-220330200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:220268600-220293800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:220269200-220291600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:220269200-220291600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:220269200-220292800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr1:220269200-220293600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:220269400-220330000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr1:220269600-220291600	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr1:220269600-220291800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:220269800-220291600	Strong transcription	Fetal Muscle Trunk	muscle
12	chr1:220269800-220292800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:220270000-220291600	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr1:220270000-220292800	Strong transcription	Primary B cells from peripheral blood	blood
15	chr1:220270400-220291600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr1:220270600-220293800	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr1:220271000-220292000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr1:220272000-220293200	Strong transcription	Dnd41	blood
19	chr1:220278600-220316200	Weak transcription	Pancreas	Pancrea
20	chr1:220281200-220295200	Weak transcription	Right Atrium	heart
21	chr1:220281400-220300600	Weak transcription	NHLF	lung
22	chr1:220281400-220307200	Weak transcription	Brain Angular Gyrus	brain
23	chr1:220281400-220307800	Weak transcription	Psoas Muscle	Psoas
24	chr1:220281400-220314400	Weak transcription	Fetal Brain Male	brain
25	chr1:220283000-220292800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr1:220283000-220292800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:220284600-220301400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr1:220284600-220305600	Weak transcription	Small Intestine	intestine
29	chr1:220284600-220307400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr1:220284600-220307800	Weak transcription	Spleen	Spleen
31	chr1:220284600-220313000	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr1:220284600-220313600	Weak transcription	Gastric	stomach
33	chr1:220284600-220324600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr1:220284800-220292400	Weak transcription	Fetal Heart	heart
35	chr1:220284800-220300000	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr1:220284800-220301600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr1:220285400-220299600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr1:220285800-220292000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr1:220286000-220291600	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr1:220286400-220292800	Strong transcription	Primary B cells from cord blood	blood
41	chr1:220286600-220291600	Strong transcription	Brain Germinal Matrix	brain
42	chr1:220286600-220291600	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr1:220286600-220292600	Strong transcription	NHDF-Ad	bronchial
44	chr1:220286800-220292000	Strong transcription	HSMM	muscle
45	chr1:220286800-220292800	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr1:220286800-220292800	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr1:220287000-220291800	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr1:220287000-220292600	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr1:220287200-220292800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr1:220287400-220291600	Strong transcription	Primary T cells from cord blood	blood

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