Variant report

Variant	rs2959056
Chromosome Location	chr11:4019401-4019402
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:3929305..3931209-chr11:4016785..4019728,2	K562	blood:
2	chr11:3861767..3864262-chr11:4018054..4019726,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177105	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10742189	0.84[TSI][hapmap]
rs11030224	0.85[CEU][hapmap]
rs11030264	0.92[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes]
rs11030394	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11030536	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11030608	0.84[EUR][1000 genomes]
rs11030842	0.89[ASW][hapmap];0.81[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.83[ASN][1000 genomes]
rs1372804	0.89[ASW][hapmap];0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.81[ASN][1000 genomes]
rs183484	0.86[CHB][hapmap]
rs1980412	0.86[CHB][hapmap];0.91[MKK][hapmap]
rs232054	0.86[CHB][hapmap]
rs2735689	0.86[CHB][hapmap]
rs2735691	0.86[CHB][hapmap];0.91[MKK][hapmap]
rs2920144	0.81[CHB][hapmap];0.95[GIH][hapmap]
rs2923944	0.96[CEU][hapmap];0.91[GIH][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2923945	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2923948	0.82[CEU][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs2923953	0.81[CHB][hapmap]
rs2923956	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2958713	0.96[CEU][hapmap];0.82[CHB][hapmap];0.90[EUR][1000 genomes]
rs2958714	0.96[CEU][hapmap];0.82[CHB][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2959065	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2959070	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2959075	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2959077	0.88[EUR][1000 genomes]
rs2959079	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2959081	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4910863	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs4910864	0.81[EUR][1000 genomes]
rs7938196	0.81[EUR][1000 genomes]
rs7945639	0.92[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][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	nsv1046065	chr11:3808818-4049150	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv540909	chr11:3808818-4049150	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv896896	chr11:4010409-4185595	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1042719	chr11:4017541-4101609	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2959056	RRM1	cis	Artery Tibial	GTEx
rs2959056	RRM1	cis	Nerve Tibial	GTEx
rs2959056	OR51A4	cis	parietal	SCAN
rs2959056	TRIM22	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3989400-4031000	Weak transcription	Aorta	Aorta
2	chr11:4006800-4022600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr11:4009400-4020200	Weak transcription	Pancreas	Pancrea
4	chr11:4011800-4027600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr11:4015600-4020400	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr11:4016000-4020400	Weak transcription	Thymus	Thymus
7	chr11:4016600-4019600	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr11:4017400-4041400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr11:4017600-4020400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr11:4017600-4020400	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr11:4017600-4020400	Weak transcription	Fetal Thymus	thymus
12	chr11:4017600-4020400	Weak transcription	Dnd41	blood
13	chr11:4017600-4020800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr11:4017600-4043400	Weak transcription	Primary B cells from cord blood	blood
15	chr11:4017800-4020200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr11:4017800-4020400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr11:4017800-4020600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr11:4018000-4020400	Weak transcription	Fetal Muscle Leg	muscle
19	chr11:4018000-4023000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr11:4018200-4020200	Weak transcription	Primary hematopoietic stem cells	blood
21	chr11:4018200-4027000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr11:4018200-4027200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr11:4018400-4027000	Weak transcription	Primary T cells from cord blood	blood
24	chr11:4018800-4020000	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr11:4018800-4022400	Weak transcription	Liver	Liver
26	chr11:4018800-4027200	Weak transcription	Psoas Muscle	Psoas
27	chr11:4019400-4020600	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr11:4019400-4027000	Weak transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links