Variant report

Variant	rs17074067
Chromosome Location	chr13:30511367-30511368
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:30508008..30510755-chr13:30510923..30512750,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-90M5.1.1-1	chr13:30511339-30511418	XLOC_010332
2	lnc-RP11-90M5.1.1-1	chr13:30511339-30511418	ENSG00000122043.6

Variant related genes	Relation type
ENSG00000122043	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10492461	1.00[ASN][1000 genomes]
rs11838968	1.00[ASN][1000 genomes]
rs11839078	1.00[ASN][1000 genomes]
rs11840419	1.00[ASN][1000 genomes]
rs11840423	1.00[ASN][1000 genomes]
rs11841787	1.00[ASN][1000 genomes]
rs11842111	1.00[ASN][1000 genomes]
rs11842198	1.00[ASN][1000 genomes]
rs11842394	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11842819	1.00[ASN][1000 genomes]
rs1557088	1.00[ASN][1000 genomes]
rs17074013	1.00[ASN][1000 genomes]
rs17074016	1.00[ASN][1000 genomes]
rs17074063	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17074065	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17074118	0.92[YRI][hapmap]
rs17074120	0.92[YRI][hapmap]
rs17074166	1.00[ASN][1000 genomes]
rs17074176	1.00[ASN][1000 genomes]
rs1998729	1.00[ASN][1000 genomes]
rs4238129	1.00[ASN][1000 genomes]
rs4578499	1.00[ASN][1000 genomes]
rs4769783	0.92[YRI][hapmap]
rs4769786	1.00[ASN][1000 genomes]
rs4769787	1.00[ASN][1000 genomes]
rs4769788	1.00[ASN][1000 genomes]
rs4769790	1.00[ASN][1000 genomes]
rs4769791	1.00[ASN][1000 genomes]
rs496557	1.00[ASN][1000 genomes]
rs524939	1.00[ASN][1000 genomes]
rs525768	1.00[ASN][1000 genomes]
rs552465	1.00[ASN][1000 genomes]
rs61285944	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs638278	1.00[ASN][1000 genomes]
rs661331	1.00[ASN][1000 genomes]
rs729285	1.00[ASN][1000 genomes]
rs73159369	1.00[ASN][1000 genomes]
rs73159387	1.00[ASN][1000 genomes]
rs73450320	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73450326	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73450335	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73450337	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73450342	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73450344	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73450347	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73450349	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs745251	1.00[ASN][1000 genomes]
rs745252	1.00[ASN][1000 genomes]
rs9506248	1.00[ASN][1000 genomes]
rs9508600	1.00[ASN][1000 genomes]
rs9508603	1.00[ASN][1000 genomes]
rs9508605	1.00[ASN][1000 genomes]
rs9508611	1.00[ASN][1000 genomes]
rs9508613	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3520592	chr13:30243601-30648554	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	esv3520593	chr13:30243601-30648554	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv510598	chr13:30476386-30542798	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30498800-30513200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr13:30509000-30512600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr13:30509400-30511600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
4	chr13:30509400-30511600	Enhancers	Liver	Liver
5	chr13:30509400-30512800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
6	chr13:30509800-30515000	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr13:30510000-30511400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr13:30510000-30511600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
9	chr13:30510000-30511800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
10	chr13:30510200-30512000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr13:30510400-30515000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr13:30510600-30511800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
13	chr13:30510600-30512000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr13:30510600-30512800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr13:30510600-30512800	Enhancers	Thymus	Thymus
16	chr13:30510600-30513000	Enhancers	Fetal Thymus	thymus
17	chr13:30510800-30511400	Weak transcription	Spleen	Spleen
18	chr13:30510800-30512000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr13:30510800-30521600	Weak transcription	Pancreas	Pancrea
20	chr13:30511000-30511400	Enhancers	Primary T cells fromperipheralblood	blood
21	chr13:30511000-30511400	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr13:30511000-30511800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
23	chr13:30511000-30512200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr13:30511000-30513000	Enhancers	Primary T cells from cord blood	blood
25	chr13:30511000-30513000	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr13:30511200-30511400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr13:30511200-30513000	Enhancers	Primary T killer memory cells from peripheral blood	blood

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