Variant report

Variant	rs17817919
Chromosome Location	chr11:85754721-85754722
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:85753274..85754881-chr11:85905097..85907303,2	MCF-7	breast:
2	chr11:85752345..85755214-chr11:85762057..85763811,2	K562	blood:
3	chr11:85753212..85755619-chr11:85956266..85958144,2	K562	blood:
4	chr11:85752985..85755269-chr11:85927440..85930207,2	MCF-7	breast:
5	chr11:85754219..85755757-chr11:85998190..86001098,2	K562	blood:
6	chr11:85753896..85756405-chr11:85894218..85896804,2	K562	blood:
7	chr11:85752945..85755603-chr11:85903337..85906078,2	K562	blood:
8	chr11:85750753..85754921-chr11:85777860..85781815,4	MCF-7	breast:
9	chr11:85752580..85755769-chr11:85817812..85820593,3	K562	blood:
10	chr11:85579605..85581387-chr11:85752967..85754863,2	MCF-7	breast:
11	chr11:85754103..85756697-chr11:85903724..85906078,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000254502	Chromatin interaction
ENSG00000254699	Chromatin interaction
ENSG00000074266	Chromatin interaction
ENSG00000073921	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10128700	0.93[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10501603	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10501605	0.94[CEU][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10501607	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10501610	1.00[LWK][hapmap]
rs10898431	0.88[CEU][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11234489	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11234492	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11234496	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11234502	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11234512	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11234513	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11234517	1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11234522	1.00[ASN][1000 genomes]
rs11234544	0.82[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs11234548	0.80[EUR][1000 genomes]
rs11825378	1.00[ASN][1000 genomes]
rs11825912	1.00[ASN][1000 genomes]
rs11828161	1.00[ASN][1000 genomes]
rs12270433	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12271390	0.80[EUR][1000 genomes]
rs12277986	0.80[EUR][1000 genomes]
rs12278260	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12279581	1.00[ASN][1000 genomes]
rs12279956	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12281494	0.87[EUR][1000 genomes]
rs12281958	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12282655	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12284629	0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs12287170	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12294130	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs1596739	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17148600	1.00[ASN][1000 genomes]
rs17159904	0.86[GIH][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs17744938	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17745105	0.94[CEU][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17745153	1.00[CEU][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17745236	1.00[CEU][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17745248	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17745273	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]
rs17817582	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17817588	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17817690	0.94[CEU][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17817859	0.94[CEU][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17817883	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17817956	0.94[CEU][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2001241	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2084077	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs41381550	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4943934	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4943936	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4943937	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs4944550	0.94[CEU][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4944551	0.87[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4944552	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944553	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4944554	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4944555	0.85[CEU][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4944556	0.88[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs55697624	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55791429	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55815523	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56026701	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56187740	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57125313	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58937798	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59019168	1.00[ASN][1000 genomes]
rs59104711	1.00[ASN][1000 genomes]
rs60253048	1.00[ASN][1000 genomes]
rs60264644	1.00[ASN][1000 genomes]
rs60737637	1.00[ASN][1000 genomes]
rs61535933	1.00[ASN][1000 genomes]
rs72949419	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72949429	0.81[AMR][1000 genomes]
rs72949443	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72950443	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72950453	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72950456	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72951266	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72951268	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72959177	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72959197	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72959906	0.87[EUR][1000 genomes]
rs72959929	0.80[EUR][1000 genomes]
rs72961110	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72961111	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72963077	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72963086	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72963092	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72965157	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72965166	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7927222	0.82[CEU][hapmap];0.86[GIH][hapmap]
rs7943152	0.87[CEU][hapmap];0.86[AFR][1000 genomes];0.87[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17817919	SYTL2	cis	cerebellum	SCAN
rs17817919	PICALM	cis	cerebellum	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85737200-85755200	Weak transcription	Lung	lung
2	chr11:85737200-85755600	Weak transcription	Esophagus	oesophagus
3	chr11:85740400-85755600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr11:85742200-85755000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr11:85742200-85755400	Weak transcription	Aorta	Aorta
6	chr11:85742600-85755600	Weak transcription	Placenta	Placenta
7	chr11:85742800-85758400	Weak transcription	Fetal Intestine Large	intestine
8	chr11:85746600-85755600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr11:85746600-85762800	Weak transcription	Stomach Mucosa	stomach
10	chr11:85746800-85755600	Weak transcription	Pancreas	Pancrea
11	chr11:85747000-85755600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr11:85749600-85755600	Weak transcription	Fetal Thymus	thymus
13	chr11:85750200-85758200	Weak transcription	Fetal Intestine Small	intestine
14	chr11:85750600-85758800	Weak transcription	Fetal Muscle Trunk	muscle
15	chr11:85751400-85761800	Enhancers	Liver	Liver
16	chr11:85751600-85755400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr11:85751600-85756400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr11:85751600-85757600	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr11:85751600-85758200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr11:85751800-85755000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr11:85751800-85755800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr11:85751800-85755800	Enhancers	Osteobl	bone
23	chr11:85751800-85756000	Enhancers	HMEC	breast
24	chr11:85751800-85756000	Enhancers	NHLF	lung
25	chr11:85751800-85760600	Enhancers	Primary T cells from cord blood	blood
26	chr11:85751800-85761200	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr11:85752000-85756000	Enhancers	NHDF-Ad	bronchial
28	chr11:85752200-85756800	Enhancers	Primary B cells from cord blood	blood
29	chr11:85752400-85758000	Enhancers	Hela-S3	cervix
30	chr11:85752400-85759000	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr11:85752400-85760600	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr11:85752400-85768400	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr11:85752600-85756000	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr11:85752600-85756000	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr11:85752800-85755200	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr11:85752800-85755800	Enhancers	HepG2	liver
37	chr11:85752800-85756200	Enhancers	Primary B cells from peripheral blood	blood
38	chr11:85752800-85758400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr11:85752800-85768200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr11:85752800-85776400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr11:85753000-85754800	Enhancers	Muscle Satellite Cultured Cells	--
42	chr11:85753000-85755200	Weak transcription	Fetal Stomach	stomach
43	chr11:85753000-85756000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr11:85753000-85756200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr11:85753000-85756200	Enhancers	HSMM	muscle
46	chr11:85753000-85763000	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr11:85753200-85754800	Weak transcription	Psoas Muscle	Psoas
48	chr11:85753200-85755000	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr11:85753200-85755200	Weak transcription	Right Atrium	heart
50	chr11:85753200-85755600	Enhancers	Colon Smooth Muscle	Colon

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