Variant report

Variant	rs3763888
Chromosome Location	chr11:35307148-35307149
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:35303293..35305865-chr11:35306107..35307804,2	MCF-7	breast:
2	chr11:35287643..35289884-chr11:35306047..35307843,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CD44-1	chr11:35306884-35307556	ENSG00000255004.1

Variant related genes	Relation type
ENSG00000255004	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1043101	1.00[CEU][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10742339	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10742340	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10742341	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10768118	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10768120	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10768121	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10768122	1.00[CEU][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10768123	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10768126	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10836360	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10836361	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10836362	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10836363	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10836364	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10836367	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10836369	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11033045	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11033046	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11033048	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11033052	0.85[YRI][hapmap]
rs11524863	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12361171	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12796856	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1570214	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1570215	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17378105	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3088168	1.00[CEU][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35629461	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3794086	0.92[CEU][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3794089	0.96[CEU][hapmap];0.80[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3794090	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3794091	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3794098	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3794099	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3794100	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3794101	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3794102	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3794103	1.00[CEU][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3818275	0.85[YRI][hapmap]
rs3847604	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4755394	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4755395	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4756203	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4756204	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4756205	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4756206	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57339940	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6484778	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7102949	0.81[YRI][hapmap]
rs7105505	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7105690	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7115246	0.96[YRI][hapmap]
rs7121587	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs736374	0.83[EUR][1000 genomes]
rs7946149	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs932633	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs932635	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs957350	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9633870	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045837	chr11:34893992-35395190	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv832120	chr11:35277410-35490304	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:35285800-35308800	Weak transcription	Gastric	stomach
2	chr11:35298000-35317200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr11:35298200-35326000	Weak transcription	Brain Substantia Nigra	brain
4	chr11:35299000-35308800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr11:35299000-35326600	Weak transcription	Brain Hippocampus Middle	brain
6	chr11:35299600-35309800	Strong transcription	Cortex derived primary cultured neurospheres	brain
7	chr11:35299800-35328600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr11:35300400-35309800	Strong transcription	Fetal Brain Female	brain
9	chr11:35302400-35327000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr11:35302600-35309800	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr11:35302600-35329000	Weak transcription	Brain Angular Gyrus	brain
12	chr11:35304000-35324800	Weak transcription	Liver	Liver
13	chr11:35304200-35309600	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr11:35304200-35309800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr11:35304200-35310600	Weak transcription	Left Ventricle	heart
16	chr11:35304600-35309600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr11:35304600-35309600	Weak transcription	HSMM	muscle
18	chr11:35304600-35309800	Weak transcription	Osteobl	bone
19	chr11:35304600-35310000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr11:35304600-35314200	Weak transcription	Stomach Mucosa	stomach
21	chr11:35304600-35317000	Weak transcription	Pancreas	Pancrea
22	chr11:35304600-35326600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr11:35304800-35309000	Weak transcription	NHDF-Ad	bronchial
24	chr11:35304800-35309800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr11:35304800-35309800	Weak transcription	NHLF	lung
26	chr11:35304800-35310000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr11:35304800-35310000	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr11:35304800-35310200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr11:35305200-35309800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr11:35305800-35308000	Strong transcription	HepG2	liver
31	chr11:35306000-35308600	Strong transcription	Brain Anterior Caudate	brain
32	chr11:35306200-35308600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr11:35306400-35308600	Strong transcription	Brain Inferior Temporal Lobe	brain
34	chr11:35307000-35308400	Strong transcription	Fetal Brain Male	brain
35	chr11:35307000-35309400	Weak transcription	HSMMtube	muscle
36	chr11:35307000-35309800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr11:35307000-35310000	Strong transcription	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links