Variant report

Variant	rs17745273
Chromosome Location	chr11:85755538-85755539
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:85753212..85755619-chr11:85956266..85958144,2	K562	blood:
2	chr11:85755134..85758081-chr11:85773891..85777241,3	K562	blood:
3	chr11:85754219..85755757-chr11:85998190..86001098,2	K562	blood:
4	chr11:85753896..85756405-chr11:85894218..85896804,2	K562	blood:
5	chr11:85752945..85755603-chr11:85903337..85906078,2	K562	blood:
6	chr11:85752580..85755769-chr11:85817812..85820593,3	K562	blood:
7	chr11:85754103..85756697-chr11:85903724..85906078,2	K562	blood:

Variant related genes	Relation type
ENSG00000254699	Chromatin interaction
ENSG00000074266	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10128700	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10501603	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10501605	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10501607	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10501610	1.00[LWK][hapmap]
rs10898431	0.83[CEU][hapmap];0.86[EUR][1000 genomes]
rs11234489	0.88[EUR][1000 genomes]
rs11234492	0.89[EUR][1000 genomes]
rs11234496	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11234502	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11234512	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11234513	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11234517	0.94[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11234544	0.88[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs11234548	0.81[EUR][1000 genomes]
rs12270433	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12271390	0.81[EUR][1000 genomes]
rs12276435	0.81[EUR][1000 genomes]
rs12277986	0.81[EUR][1000 genomes]
rs12278260	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12279956	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12281494	0.88[EUR][1000 genomes]
rs12281958	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12282655	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12284629	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs12287170	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12294130	0.82[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs1596739	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17159904	0.86[GIH][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs17744938	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17745105	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17745153	0.94[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17745236	0.93[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17745248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17817582	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17817588	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17817690	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17817859	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17817883	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17817919	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17817956	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2001241	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2084077	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs41381550	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4943934	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4943936	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4943937	0.93[CEU][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs4944550	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4944551	0.93[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4944552	0.94[CEU][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4944553	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4944554	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4944555	0.92[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4944556	0.94[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs55697624	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55791429	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55815523	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56026701	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56187740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56207019	0.81[EUR][1000 genomes]
rs57125313	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58937798	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7128598	0.81[EUR][1000 genomes]
rs72949419	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72949429	0.81[AMR][1000 genomes]
rs72949443	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72950443	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72950453	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72950456	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72951266	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72951268	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72959177	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72959197	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72959906	0.88[EUR][1000 genomes]
rs72959929	0.81[EUR][1000 genomes]
rs72961110	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72961111	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72963077	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72963086	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72963092	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72965157	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72965166	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7927222	0.88[CEU][hapmap];0.86[GIH][hapmap]
rs7943152	0.94[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035489	chr11:85502953-85778229	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1053808	chr11:85588919-85757693	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv468769	chr11:85683554-85757589	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv555641	chr11:85683554-85757589	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv898054	chr11:85683554-85772636	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv468771	chr11:85688209-85757589	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv468773	chr11:85688209-85757589	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv555643	chr11:85688209-85757589	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv468774	chr11:85688209-85775059	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv555644	chr11:85688209-85775059	Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	esv1829985	chr11:85740319-85789350	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17745273	SYTL2	cis	cerebellum	SCAN
rs17745273	CCDC83	cis	parietal	SCAN
rs17745273	FAM181B	cis	parietal	SCAN
rs17745273	GRM5	cis	cerebellum	SCAN
rs17745273	PICALM	cis	cerebellum	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85737200-85755600	Weak transcription	Esophagus	oesophagus
2	chr11:85740400-85755600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr11:85742600-85755600	Weak transcription	Placenta	Placenta
4	chr11:85742800-85758400	Weak transcription	Fetal Intestine Large	intestine
5	chr11:85746600-85755600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr11:85746600-85762800	Weak transcription	Stomach Mucosa	stomach
7	chr11:85746800-85755600	Weak transcription	Pancreas	Pancrea
8	chr11:85747000-85755600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr11:85749600-85755600	Weak transcription	Fetal Thymus	thymus
10	chr11:85750200-85758200	Weak transcription	Fetal Intestine Small	intestine
11	chr11:85750600-85758800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr11:85751400-85761800	Enhancers	Liver	Liver
13	chr11:85751600-85756400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr11:85751600-85757600	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr11:85751600-85758200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr11:85751800-85755800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr11:85751800-85755800	Enhancers	Osteobl	bone
18	chr11:85751800-85756000	Enhancers	HMEC	breast
19	chr11:85751800-85756000	Enhancers	NHLF	lung
20	chr11:85751800-85760600	Enhancers	Primary T cells from cord blood	blood
21	chr11:85751800-85761200	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr11:85752000-85756000	Enhancers	NHDF-Ad	bronchial
23	chr11:85752200-85756800	Enhancers	Primary B cells from cord blood	blood
24	chr11:85752400-85758000	Enhancers	Hela-S3	cervix
25	chr11:85752400-85759000	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr11:85752400-85760600	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr11:85752400-85768400	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr11:85752600-85756000	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr11:85752600-85756000	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr11:85752800-85755800	Enhancers	HepG2	liver
31	chr11:85752800-85756200	Enhancers	Primary B cells from peripheral blood	blood
32	chr11:85752800-85758400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr11:85752800-85768200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr11:85752800-85776400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr11:85753000-85756000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr11:85753000-85756200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr11:85753000-85756200	Enhancers	HSMM	muscle
38	chr11:85753000-85763000	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr11:85753200-85755600	Enhancers	Colon Smooth Muscle	Colon
40	chr11:85753200-85755800	Enhancers	A549	lung
41	chr11:85753200-85756600	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr11:85753200-85758600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr11:85753200-85759000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr11:85753200-85762200	Enhancers	Adipose Nuclei	Adipose
45	chr11:85753200-85764600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr11:85753200-85768000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr11:85753400-85758000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr11:85753600-85755800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr11:85753800-85755600	Enhancers	Duodenum Mucosa	Duodenum
50	chr11:85753800-85756000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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