Variant report

Variant	rs1883593
Chromosome Location	chr6:24647191-24647192
allele	A/T
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	FOS	chr6:24646991-24647365	MCF10A-Er-Src	breast:	n/a	chr6:24647170-24647178 chr6:24647168-24647180
2	JUND	chr6:24646982-24647384	MCF-7	breast:	n/a	chr6:24647170-24647178 chr6:24647168-24647180
3	GATA3	chr6:24646823-24647455	MCF-7	breast:	n/a	chr6:24647171-24647180
4	STAT3	chr6:24647064-24647285	MCF10A-Er-Src	breast:	n/a	n/a
5	MXI1	chr6:24645895-24647439	IMR90	lung:	n/a	chr6:24646440-24646455 chr6:24646438-24646453
6	STAT3	chr6:24647064-24647298	MCF10A-Er-Src	breast:	n/a	n/a
7	STAT3	chr6:24647094-24647303	MCF10A-Er-Src	breast:	n/a	n/a
8	RFX5	chr6:24645329-24647270	Hela-S3	cervix:	n/a	chr6:24646439-24646454 chr6:24646439-24646454 chr6:24646438-24646455 chr6:24646439-24646454
9	FOS	chr6:24647011-24647358	MCF10A-Er-Src	breast:	n/a	chr6:24647170-24647178 chr6:24647168-24647180
10	FOS	chr6:24647013-24647353	MCF10A-Er-Src	breast:	n/a	chr6:24647170-24647178 chr6:24647168-24647180
11	EP300	chr6:24647040-24647311	Hela-S3	cervix:	n/a	n/a
12	FOSL2	chr6:24646958-24647404	MCF-7	breast:	n/a	chr6:24647170-24647178 chr6:24647168-24647180
13	FOS	chr6:24646990-24647355	MCF10A-Er-Src	breast:	n/a	chr6:24647170-24647178 chr6:24647168-24647180
14	JUND	chr6:24647013-24647338	Hela-S3	cervix:	n/a	chr6:24647170-24647178 chr6:24647168-24647180
15	JUND	chr6:24646868-24647528	MCF-7	breast:	n/a	chr6:24647170-24647178 chr6:24647168-24647180
16	ZNF217	chr6:24647078-24647336	MCF-7	breast:	n/a	n/a
17	MAZ	chr6:24647008-24647196	GM12878	blood:	n/a	n/a
18	FOSL2	chr6:24646888-24647436	MCF-7	breast:	n/a	chr6:24647170-24647178 chr6:24647168-24647180
19	STAT3	chr6:24647049-24647292	MCF10A-Er-Src	breast:	n/a	n/a
20	GATA3	chr6:24646895-24647529	MCF-7	breast:	n/a	chr6:24647171-24647180
21	SIN3AK20	chr6:24646862-24647478	MCF-7	breast:	n/a	n/a
22	RCOR1	chr6:24645653-24647241	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:24644992..24647314-chr6:24719656..24721157,2	MCF-7	breast:
2	chr6:24645396..24648521-chr6:24658092..24661192,3	K562	blood:
3	chr6:24645218..24647641-chr6:24665331..24668427,5	MCF-7	breast:
4	chr6:24645863..24648986-chr6:24665821..24668897,5	MCF-7	breast:
5	chr6:24646579..24649824-chr6:24666656..24668956,3	K562	blood:
6	chr6:24645396..24648552-chr6:24658188..24661192,4	K562	blood:
7	chr6:24645670..24648708-chr6:24654981..24659486,5	MCF-7	breast:

Variant related genes	Relation type
KIAA0319	TF binding region
ENSG00000111802	Chromatin interaction
ENSG00000112304	Chromatin interaction
ENSG00000112308	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs3181228	0.82[CHB][hapmap]
rs4544900	0.82[CHB][hapmap]
rs6917209	0.81[CHB][hapmap]
rs7765904	0.82[CHB][hapmap]
rs9366577	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9379685	0.82[CHB][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	esv3508002	chr6:24618580-24732946	Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv3508003	chr6:24618580-24732946	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv601164	chr6:24625091-24661599	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	nsv601165	chr6:24632642-24666007	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1883593	C6orf62	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24646000-24647200	Active TSS	Fetal Kidney	kidney
2	chr6:24646400-24658800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:24646600-24647200	Flanking Active TSS	Hela-S3	cervix
4	chr6:24646600-24652200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr6:24646600-24655800	Weak transcription	Aorta	Aorta
6	chr6:24646800-24647200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:24646800-24647200	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr6:24646800-24647200	Enhancers	HMEC	breast
9	chr6:24646800-24647200	Enhancers	NH-A	brain
10	chr6:24646800-24647200	Enhancers	NHDF-Ad	bronchial
11	chr6:24646800-24649400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr6:24646800-24649400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr6:24646800-24650000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:24646800-24650000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr6:24646800-24650200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr6:24646800-24650200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr6:24646800-24650400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr6:24646800-24650400	Weak transcription	Colon Smooth Muscle	Colon
19	chr6:24646800-24650400	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr6:24646800-24650400	Weak transcription	HSMM	muscle
21	chr6:24646800-24650600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr6:24646800-24650600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr6:24646800-24650600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr6:24646800-24650800	Weak transcription	Fetal Muscle Trunk	muscle
25	chr6:24646800-24651800	Weak transcription	Fetal Stomach	stomach
26	chr6:24646800-24651800	Weak transcription	Left Ventricle	heart
27	chr6:24646800-24651800	Weak transcription	Psoas Muscle	Psoas
28	chr6:24646800-24652000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr6:24646800-24652000	Weak transcription	Ovary	ovary
30	chr6:24646800-24652400	Weak transcription	Fetal Lung	lung
31	chr6:24646800-24652600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:24646800-24652600	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr6:24646800-24653000	Weak transcription	HSMMtube	muscle
34	chr6:24646800-24653200	Weak transcription	Fetal Brain Male	brain
35	chr6:24646800-24653200	Weak transcription	Gastric	stomach
36	chr6:24646800-24655600	Weak transcription	Pancreas	Pancrea
37	chr6:24646800-24662400	Weak transcription	Right Ventricle	heart
38	chr6:24646800-24662600	Weak transcription	Spleen	Spleen
39	chr6:24646800-24666000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr6:24647000-24647200	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr6:24647000-24647200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr6:24647000-24647200	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr6:24647000-24647200	Enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr6:24647000-24647200	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr6:24647000-24647200	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr6:24647000-24647200	Enhancers	Primary B cells from peripheral blood	blood
47	chr6:24647000-24647200	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr6:24647000-24647200	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr6:24647000-24647200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr6:24647000-24647200	Enhancers	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links