Variant report

Variant	rs6109784
Chromosome Location	chr20:1377937-1377938
allele	C/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	GATA2	chr20:1376926-1377938	HUVEC	blood vessel:	n/a	n/a
2	CTCF	chr20:1377929-1378909	A549	lung:	n/a	n/a
3	TCF12	chr20:1376863-1377958	SK-N-SH	brain:	n/a	n/a
4	MAX	chr20:1377747-1378064	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:1311170..1313178-chr20:1375067..1377982,2	MCF-7	breast:
2	chr20:1372265..1374916-chr20:1377104..1379647,4	MCF-7	breast:

Variant related genes	Relation type
FKBP1A	TF binding region
ENSG00000088832	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10485824	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11087048	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11697322	1.00[CHB][hapmap]
rs11697395	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11697973	1.00[ASN][1000 genomes]
rs11697987	1.00[ASN][1000 genomes]
rs11698000	1.00[ASN][1000 genomes]
rs11699494	1.00[CHB][hapmap]
rs13163	1.00[CHB][hapmap]
rs13433171	1.00[ASN][1000 genomes]
rs16994239	1.00[CHB][hapmap]
rs16994549	1.00[CHB][hapmap]
rs16995146	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs16995228	1.00[ASN][1000 genomes]
rs16995310	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs16995332	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17793560	1.00[CHB][hapmap]
rs17794135	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1883933	1.00[CHB][hapmap]
rs1884390	1.00[CHB][hapmap]
rs2064645	1.00[CHB][hapmap]
rs2064646	1.00[CHB][hapmap]
rs2249832	1.00[CHB][hapmap]
rs2250091	1.00[CHB][hapmap]
rs2253429	1.00[CHB][hapmap]
rs2253431	1.00[CHB][hapmap]
rs2253693	1.00[CHB][hapmap]
rs2253698	1.00[CHB][hapmap]
rs2256095	1.00[CHB][hapmap]
rs2256229	1.00[CHB][hapmap]
rs2256240	1.00[CHB][hapmap]
rs2256243	1.00[CHB][hapmap]
rs2256250	1.00[CHB][hapmap]
rs2256251	1.00[CHB][hapmap]
rs2263656	1.00[CHB][hapmap]
rs2873522	1.00[CHB][hapmap]
rs33999287	1.00[ASN][1000 genomes]
rs35442028	1.00[ASN][1000 genomes]
rs4536713	1.00[ASN][1000 genomes]
rs45512895	1.00[ASN][1000 genomes]
rs4577347	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4813115	1.00[CHB][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4814102	1.00[CHB][hapmap]
rs56035174	1.00[ASN][1000 genomes]
rs57806058	1.00[ASN][1000 genomes]
rs59377624	1.00[ASN][1000 genomes]
rs59681252	1.00[ASN][1000 genomes]
rs6033534	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6033554	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6033660	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6033672	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033871	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6033896	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6033914	1.00[CHB][hapmap]
rs6033935	1.00[CHB][hapmap]
rs6041382	1.00[ASN][1000 genomes]
rs6041689	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6041716	1.00[CHB][hapmap]
rs6041717	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6042000	1.00[ASN][1000 genomes]
rs6042506	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6042550	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6042568	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6042574	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6042578	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6042585	1.00[CHB][hapmap]
rs6042588	1.00[CHB][hapmap]
rs6042676	1.00[CHB][hapmap]
rs6042689	1.00[CHB][hapmap]
rs6078575	1.00[CHB][hapmap]
rs6105031	1.00[CHB][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6105101	1.00[CHB][hapmap]
rs6109437	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6109511	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6109522	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6109740	1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6109984	1.00[CHB][hapmap]
rs6109989	1.00[CHB][hapmap]
rs6110189	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6110193	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs62187542	1.00[ASN][1000 genomes]
rs62187543	1.00[ASN][1000 genomes]
rs62623705	1.00[ASN][1000 genomes]
rs6514337	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6514364	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs715217	1.00[CHB][hapmap]
rs7271240	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7274052	1.00[ASN][1000 genomes]
rs73067251	1.00[ASN][1000 genomes]
rs73069188	1.00[ASN][1000 genomes]
rs73076965	1.00[ASN][1000 genomes]
rs73076966	1.00[ASN][1000 genomes]
rs73579382	1.00[ASN][1000 genomes]
rs73581208	1.00[ASN][1000 genomes]
rs747611	1.00[CHB][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8117563	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs8117744	1.00[ASN][1000 genomes]
rs8118276	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs8119259	1.00[ASN][1000 genomes]
rs912113	1.00[CHB][hapmap]
rs958839	1.00[CHB][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522008	chr20:1340390-1638578	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Active TSS 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	28 gene(s)	inside rSNPs	diseases
2	esv3400839	chr20:1377767-1383335	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1374400-1379600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr20:1374400-1381400	Weak transcription	Gastric	stomach
3	chr20:1374600-1378000	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr20:1374600-1378600	Weak transcription	K562	blood
5	chr20:1374600-1378800	Weak transcription	Duodenum Mucosa	Duodenum
6	chr20:1374600-1379000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr20:1374600-1379400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr20:1374600-1380000	Weak transcription	Liver	Liver
9	chr20:1374600-1380200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr20:1374800-1379400	Weak transcription	Colonic Mucosa	Colon
11	chr20:1374800-1382800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr20:1374800-1383000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr20:1375200-1379400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr20:1375400-1379000	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr20:1376000-1379200	Enhancers	Dnd41	blood
16	chr20:1376200-1378800	Weak transcription	Primary B cells from peripheral blood	blood
17	chr20:1377000-1378000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr20:1377400-1378000	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr20:1377400-1378000	Enhancers	Fetal Thymus	thymus
20	chr20:1377400-1378200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr20:1377400-1379600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr20:1377600-1379400	Weak transcription	NHEK	skin
23	chr20:1377600-1379600	Weak transcription	HMEC	breast
24	chr20:1377600-1383000	Enhancers	HUVEC	blood vessel
25	chr20:1377800-1378000	Bivalent Enhancer	Left Ventricle	heart
26	chr20:1377800-1378000	Enhancers	Lung	lung
27	chr20:1377800-1378000	Bivalent Enhancer	HepG2	liver
28	chr20:1377800-1382800	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr20:1377800-1382800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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