Variant report

Variant	rs9526567
Chromosome Location	chr13:50093452-50093453
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:50017488..50019349-chr13:50091764..50095286,3	MCF-7	breast:
2	chr13:50071845..50075663-chr13:50092471..50095842,3	K562	blood:
3	chr13:50091935..50095583-chr13:50159811..50161648,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136169	Chromatin interaction
ENSG00000102547	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1046027	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1046028	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1046295	0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1062979	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12146924	0.90[JPT][hapmap]
rs17073051	0.92[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1925742	0.94[JPT][hapmap]
rs2038881	0.83[JPT][hapmap]
rs2274276	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2980	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2981	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3033	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3186012	0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3186013	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3186024	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3764084	0.81[AFR][1000 genomes]
rs3765526	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3829366	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4340215	0.96[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4430650	0.96[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4942833	0.92[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4942836	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4942838	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4942839	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4942840	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4942843	0.95[JPT][hapmap]
rs6561533	0.92[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap]
rs6561534	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67307832	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7139494	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7317982	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7322077	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7322908	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7323493	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7323716	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7331262	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7331330	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7333969	0.89[JPT][hapmap]
rs7337718	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7339167	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7988427	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7989504	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7990988	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7991031	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7995684	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7996994	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs942870	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9526565	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9526566	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9526568	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535254	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9535255	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535256	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535257	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9535258	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9805560	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	nsv1047311	chr13:49895019-50224227	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv916093	chr13:50050919-50290245	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1036135	chr13:50071310-50183103	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv541770	chr13:50071310-50183103	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9526567	PHF11	Cis_1M	lymphoblastoid	RTeQTL
rs9526567	CAB39L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50070800-50095600	Weak transcription	Fetal Kidney	kidney
2	chr13:50075000-50102400	Weak transcription	NH-A	brain
3	chr13:50075000-50143800	Weak transcription	Small Intestine	intestine
4	chr13:50077600-50114000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr13:50080000-50107000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr13:50080200-50104600	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr13:50080600-50098000	Strong transcription	Primary B cells from cord blood	blood
8	chr13:50080600-50101000	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr13:50080600-50104600	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr13:50082200-50096200	Weak transcription	HUVEC	blood vessel
11	chr13:50083600-50103600	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr13:50083800-50099600	Strong transcription	Primary T cells from cord blood	blood
13	chr13:50084000-50104800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr13:50084800-50104200	Strong transcription	GM12878-XiMat	blood
15	chr13:50085000-50098200	Strong transcription	Dnd41	blood
16	chr13:50085000-50099600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr13:50085400-50104800	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr13:50085800-50099000	Weak transcription	Hela-S3	cervix
19	chr13:50086400-50096200	Strong transcription	Primary B cells from peripheral blood	blood
20	chr13:50086400-50097200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr13:50086400-50113600	Weak transcription	Brain Angular Gyrus	brain
22	chr13:50086600-50098400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr13:50086600-50101600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr13:50086600-50103200	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr13:50086600-50106200	Strong transcription	Fetal Thymus	thymus
26	chr13:50086600-50108800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr13:50086600-50114200	Weak transcription	Fetal Brain Female	brain
28	chr13:50086800-50093600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr13:50086800-50096200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr13:50086800-50101600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr13:50087400-50099400	Strong transcription	Liver	Liver
32	chr13:50087400-50099400	Strong transcription	Placenta	Placenta
33	chr13:50087600-50095800	Strong transcription	Duodenum Mucosa	Duodenum
34	chr13:50087800-50095800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
35	chr13:50087800-50098000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr13:50087800-50103600	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr13:50088200-50113600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr13:50088400-50151000	Weak transcription	Psoas Muscle	Psoas
39	chr13:50088600-50093600	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr13:50088600-50093600	Weak transcription	NHLF	lung
41	chr13:50088600-50134200	Weak transcription	Stomach Mucosa	stomach
42	chr13:50088800-50095600	Weak transcription	HMEC	breast
43	chr13:50088800-50097600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr13:50089200-50107400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr13:50089400-50114200	Weak transcription	Colon Smooth Muscle	Colon
46	chr13:50089600-50094600	Weak transcription	HSMM	muscle
47	chr13:50089800-50101200	Weak transcription	NHEK	skin
48	chr13:50090000-50093800	Weak transcription	Pancreas	Pancrea
49	chr13:50090000-50096200	Weak transcription	Brain Hippocampus Middle	brain
50	chr13:50090000-50101200	Weak transcription	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links