Variant report

Variant	rs1393563
Chromosome Location	chr9:85646987-85646988
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:85618969..85620782-chr9:85645693..85647630,2	MCF-7	breast:
2	chr9:85646151..85647909-chr9:85674836..85678047,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C9orf103-6	chr9:85646719-85647191	predAs_chen_BX118193_1

Variant related genes	Relation type
ENSG00000165105	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1008171	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1010480	0.89[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10116216	0.85[CEU][hapmap]
rs10116254	0.89[CEU][hapmap];0.86[AMR][1000 genomes]
rs10121204	0.88[CEU][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10121376	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10121395	0.89[CEU][hapmap];0.85[AMR][1000 genomes]
rs10126033	0.86[AMR][1000 genomes]
rs10735559	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs10746694	0.84[AMR][1000 genomes]
rs10780561	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs10780562	0.92[CEU][hapmap]
rs10780563	0.89[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10780564	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10780565	0.89[CEU][hapmap];0.86[AMR][1000 genomes]
rs10780567	0.89[CEU][hapmap]
rs10867924	0.86[AMR][1000 genomes]
rs10867925	0.82[AMR][1000 genomes]
rs10867927	0.85[AMR][1000 genomes]
rs10867928	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10867929	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs10867930	0.89[CEU][hapmap];0.81[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1125915	0.93[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13302349	0.86[AMR][1000 genomes]
rs1393562	0.89[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1393564	0.82[CEU][hapmap]
rs1393565	0.89[CEU][hapmap]
rs1502682	0.89[CEU][hapmap];0.83[AMR][1000 genomes]
rs1502683	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs1502684	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs1502685	0.89[CEU][hapmap];0.83[AMR][1000 genomes]
rs1546315	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1546316	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1546317	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1580881	0.89[CEU][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1976455	0.89[CEU][hapmap];0.82[AMR][1000 genomes]
rs1995423	0.88[CEU][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2062761	0.92[CEU][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2279814	0.89[CEU][hapmap]
rs4146960	0.88[CEU][hapmap];0.85[AMR][1000 genomes]
rs4146961	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4301515	0.89[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4348583	0.85[CEU][hapmap];0.86[AMR][1000 genomes]
rs4355855	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs4385545	0.89[CEU][hapmap]
rs4391505	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs4460464	0.85[CEU][hapmap]
rs4623517	0.89[CEU][hapmap]
rs4628323	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4877244	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4877724	0.83[EUR][1000 genomes]
rs4877725	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs4877726	0.89[CEU][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6559693	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6559694	0.89[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6559695	0.96[CEU][hapmap];0.86[AMR][1000 genomes]
rs7019227	0.89[CEU][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7024864	0.89[CEU][hapmap];0.83[AMR][1000 genomes]
rs7847666	0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7849126	0.82[EUR][1000 genomes]
rs7853052	0.84[EUR][1000 genomes]
rs7854101	0.89[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7862012	0.83[EUR][1000 genomes]
rs7864688	0.87[EUR][1000 genomes]
rs7866666	0.89[CEU][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7867614	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7872982	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs871512	0.88[CEU][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs952450	0.89[CEU][hapmap];0.86[AMR][1000 genomes]
rs998119	0.83[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893511	chr9:85495968-85833127	Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:85640400-85656400	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr9:85644200-85649600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr9:85644200-85654800	Weak transcription	Fetal Intestine Small	intestine
4	chr9:85644800-85648400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr9:85644800-85670600	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr9:85645000-85647000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr9:85645000-85647000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr9:85645000-85647000	Weak transcription	NHEK	skin
9	chr9:85645000-85648400	Weak transcription	HMEC	breast
10	chr9:85645000-85649000	Weak transcription	A549	lung
11	chr9:85645200-85649000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr9:85645400-85647400	Enhancers	Gastric	stomach
13	chr9:85645600-85662800	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr9:85645800-85647400	Enhancers	Stomach Mucosa	stomach
15	chr9:85646800-85648400	Weak transcription	Pancreas	Pancrea

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