Variant report

Variant	rs17510841
Chromosome Location	chr11:59534360-59534361
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:59533582..59535558-chr11:59538883..59542385,3	K562	blood:
2	chr11:59533196..59536602-chr11:59539532..59544445,5	MCF-7	breast:
3	chr11:59528968..59531092-chr11:59531275..59534785,3	MCF-7	breast:
4	chr11:59532568..59535193-chr11:59553721..59556232,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166900	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10501380	1.00[CEU][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs11230019	0.84[EUR][1000 genomes]
rs11230020	1.00[TSI][hapmap]
rs11230036	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs11230037	1.00[TSI][hapmap]
rs1151063	1.00[TSI][hapmap]
rs1151064	1.00[TSI][hapmap]
rs11821465	1.00[TSI][hapmap]
rs12276505	1.00[CEU][hapmap]
rs12278910	1.00[TSI][hapmap]
rs12287696	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs12289921	1.00[TSI][hapmap]
rs12290453	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12291415	0.89[EUR][1000 genomes]
rs1287111	1.00[TSI][hapmap]
rs17153910	1.00[TSI][hapmap]
rs17154005	0.89[EUR][1000 genomes]
rs17154053	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17154134	1.00[TSI][hapmap]
rs17154146	1.00[TSI][hapmap]
rs17154157	1.00[TSI][hapmap]
rs17154165	1.00[TSI][hapmap]
rs17154180	1.00[TSI][hapmap]
rs17154200	1.00[TSI][hapmap]
rs17154227	1.00[TSI][hapmap]
rs17154234	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs17508845	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs17509520	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17511545	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17511686	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17593682	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs17593836	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs17594827	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17596359	0.84[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17596862	1.00[CEU][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs17597065	1.00[CEU][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs17597092	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1938690	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs2085962	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2508335	1.00[CEU][hapmap]
rs2509274	1.00[TSI][hapmap]
rs2509275	1.00[TSI][hapmap]
rs2509279	1.00[CEU][hapmap]
rs35211634	1.00[TSI][hapmap]
rs41384548	1.00[TSI][hapmap]
rs472177	1.00[TSI][hapmap]
rs473490	1.00[TSI][hapmap]
rs475800	0.83[EUR][1000 genomes]
rs479264	0.83[EUR][1000 genomes]
rs482355	1.00[TSI][hapmap]
rs482356	1.00[TSI][hapmap]
rs484814	0.83[EUR][1000 genomes]
rs485803	1.00[CEU][hapmap]
rs488331	1.00[TSI][hapmap]
rs495564	1.00[TSI][hapmap]
rs497596	0.83[EUR][1000 genomes]
rs498099	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs512194	1.00[TSI][hapmap]
rs513979	1.00[CEU][hapmap]
rs523016	1.00[TSI][hapmap]
rs524102	1.00[CEU][hapmap]
rs529270	1.00[TSI][hapmap]
rs533166	1.00[CEU][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs536544	1.00[CEU][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs540684	1.00[TSI][hapmap]
rs540989	0.83[EUR][1000 genomes]
rs549086	1.00[CEU][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs552601	1.00[TSI][hapmap]
rs554848	1.00[TSI][hapmap]
rs563800	0.83[EUR][1000 genomes]
rs579373	1.00[TSI][hapmap]
rs7101580	0.89[EUR][1000 genomes]
rs7108731	1.00[ASN][1000 genomes]
rs7112355	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs7117509	0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7119530	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7123969	1.00[TSI][hapmap]
rs7130130	0.84[EUR][1000 genomes]
rs7924849	0.84[EUR][1000 genomes]
rs7929816	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7947514	1.00[TSI][hapmap]
rs7948041	0.84[EUR][1000 genomes]
rs7948635	0.81[EUR][1000 genomes]
rs7952024	1.00[TSI][hapmap]
rs7952380	0.84[EUR][1000 genomes]
rs8280	1.00[TSI][hapmap]
rs997788	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046086	chr11:59520424-59561455	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17510841	CABLES1	trans	brain	seeQTL
rs17510841	CD44	trans	lymphoblastoid	seeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:59524000-59539200	Weak transcription	Liver	Liver
2	chr11:59524200-59545200	Weak transcription	Brain Hippocampus Middle	brain
3	chr11:59524400-59542200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr11:59524400-59545600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr11:59524400-59557000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr11:59524600-59537200	Weak transcription	NHLF	lung
7	chr11:59524600-59538400	Weak transcription	Brain Anterior Caudate	brain
8	chr11:59524600-59557400	Weak transcription	Colon Smooth Muscle	Colon
9	chr11:59524600-59573800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr11:59524800-59536400	Weak transcription	NHDF-Ad	bronchial
11	chr11:59524800-59539400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr11:59524800-59540600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr11:59524800-59543000	Weak transcription	A549	lung
14	chr11:59524800-59543800	Weak transcription	NH-A	brain
15	chr11:59524800-59553400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr11:59524800-59555400	Weak transcription	Stomach Smooth Muscle	stomach
17	chr11:59525000-59539000	Weak transcription	HUVEC	blood vessel
18	chr11:59525200-59537400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr11:59525200-59540600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr11:59525200-59543600	Weak transcription	Hela-S3	cervix
21	chr11:59525400-59540600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr11:59525400-59543400	Weak transcription	HMEC	breast
23	chr11:59525400-59551200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr11:59525600-59557800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr11:59526000-59541600	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr11:59527800-59541800	Weak transcription	Fetal Stomach	stomach
27	chr11:59529400-59541000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr11:59530000-59540600	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr11:59530400-59540600	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr11:59530400-59540600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr11:59530600-59538400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr11:59530800-59540400	Weak transcription	NHEK	skin
33	chr11:59530800-59545000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr11:59531000-59540200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr11:59531000-59541600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr11:59531600-59536800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr11:59532000-59536000	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr11:59532000-59536400	Enhancers	Fetal Intestine Large	intestine
39	chr11:59532000-59539600	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr11:59532000-59543800	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr11:59532400-59535200	Enhancers	Rectal Mucosa Donor 29	rectum
42	chr11:59532600-59535000	Enhancers	Placenta	Placenta
43	chr11:59532600-59535400	Enhancers	Small Intestine	intestine
44	chr11:59532600-59535800	Enhancers	Stomach Mucosa	stomach
45	chr11:59532600-59536400	Enhancers	Left Ventricle	heart
46	chr11:59532600-59538200	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr11:59532800-59534400	Enhancers	K562	blood
48	chr11:59532800-59534600	Enhancers	Colonic Mucosa	Colon
49	chr11:59532800-59534800	Enhancers	Ovary	ovary
50	chr11:59532800-59535200	Enhancers	Pancreas	Pancrea

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