Variant report

Variant	rs540063
Chromosome Location	chr11:85448905-85448906
allele	C/T
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:85445267..85447565-chr11:85447614..85449688,2	MCF-7	breast:
2	chr11:85447110..85449601-chr11:85539919..85542813,2	MCF-7	breast:
3	chr11:85447416..85450012-chr11:85465090..85467738,2	MCF-7	breast:
4	chr11:85446570..85449228-chr11:85451047..85454870,3	MCF-7	breast:
5	chr11:85448431..85450003-chr11:85541669..85543570,2	MCF-7	breast:
6	chr11:85447411..85449377-chr11:85521136..85523499,2	MCF-7	breast:
7	chr11:85445724..85449951-chr11:85518014..85522628,5	MCF-7	breast:
8	chr11:85447296..85450521-chr11:85450822..85453106,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000137501	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1046216	0.86[JPT][hapmap]
rs10898410	0.81[CHB][hapmap]
rs11603256	0.82[CHD][hapmap];0.91[JPT][hapmap]
rs11606656	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs1237203	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs1445497	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs188311	0.87[CEU][hapmap]
rs2044391	0.86[CHB][hapmap]
rs2196168	0.91[JPT][hapmap]
rs2374683	0.81[CHB][hapmap]
rs290173	0.81[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap]
rs290175	0.87[CEU][hapmap]
rs290184	0.85[CHD][hapmap];0.86[JPT][hapmap]
rs290185	0.84[CHD][hapmap];0.91[JPT][hapmap]
rs290190	0.83[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap]
rs290193	0.85[CHD][hapmap]
rs290194	0.91[CEU][hapmap]
rs290195	0.91[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap]
rs290196	0.87[CEU][hapmap]
rs290198	0.83[CHD][hapmap]
rs290199	0.91[CEU][hapmap]
rs290200	0.92[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs290202	0.84[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.84[TSI][hapmap]
rs370385	0.95[JPT][hapmap]
rs3753050	0.85[CHD][hapmap];0.91[JPT][hapmap]
rs3781815	0.89[JPT][hapmap]
rs3824956	0.85[CHD][hapmap];0.86[JPT][hapmap]
rs3862782	0.91[JPT][hapmap]
rs475380	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs475491	0.86[ASN][1000 genomes]
rs478089	0.91[ASN][1000 genomes]
rs491867	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4944538	0.86[CHB][hapmap]
rs496187	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs510948	0.87[CEU][hapmap]
rs520500	0.90[ASN][1000 genomes]
rs520629	0.91[CEU][hapmap]
rs537266	0.91[CEU][hapmap]
rs537604	0.87[CEU][hapmap]
rs550404	0.92[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs556669	0.92[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs570394	0.83[ASN][1000 genomes]
rs573766	0.87[CEU][hapmap]
rs575013	0.82[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs578324	0.91[CEU][hapmap]
rs580459	0.92[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs583122	0.95[CEU][hapmap]
rs588968	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs589327	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs592460	0.86[JPT][hapmap]
rs592712	0.87[CEU][hapmap]
rs596029	0.86[ASN][1000 genomes]
rs597480	0.88[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap];0.81[ASN][1000 genomes]
rs609012	0.91[CEU][hapmap]
rs613973	0.91[CEU][hapmap]
rs630613	0.81[CHB][hapmap]
rs631410	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs639688	0.95[CEU][hapmap];0.81[MEX][hapmap]
rs641393	0.88[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap];0.81[ASN][1000 genomes]
rs644972	0.96[CEU][hapmap];0.81[CHB][hapmap]
rs647175	0.86[ASN][1000 genomes]
rs647912	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.90[ASN][1000 genomes]
rs650036	0.91[CEU][hapmap]
rs653559	0.96[CEU][hapmap]
rs675513	0.86[ASN][1000 genomes]
rs678723	0.91[ASN][1000 genomes]
rs679204	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs680498	0.91[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs681044	0.91[CEU][hapmap]
rs688689	0.80[ASN][1000 genomes]
rs688741	0.91[CEU][hapmap]
rs689093	0.86[ASN][1000 genomes]
rs7103790	0.86[CHB][hapmap];0.88[CHD][hapmap];0.83[TSI][hapmap]
rs7107788	0.85[CHD][hapmap];0.91[JPT][hapmap]
rs7116195	0.86[JPT][hapmap]
rs881120	0.86[JPT][hapmap]
rs956202	0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:31 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051155	chr11:85006564-85721261	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv541110	chr11:85006564-85721261	Enhancers Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	esv2758279	chr11:85180480-85603988	Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv2759845	chr11:85180480-85603988	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv832222	chr11:85405712-85603981	Enhancers Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv898050	chr11:85406915-85499290	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1052123	chr11:85425856-85471132	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv555633	chr11:85426330-85473883	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1036110	chr11:85429074-85471132	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1054027	chr11:85429074-85477283	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	esv3471508	chr11:85429687-85472395	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	esv3471519	chr11:85429687-85472395	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv555634	chr11:85430397-85464922	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv555635	chr11:85430397-85470893	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv555636	chr11:85431886-85465179	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv1042192	chr11:85433687-85464922	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	nsv1039118	chr11:85433687-85468605	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	nsv1039830	chr11:85433687-85470589	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	nsv1047001	chr11:85433687-85470941	Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
20	nsv1042942	chr11:85433687-85471132	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
21	nsv1052732	chr11:85434057-85468605	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
22	nsv1048844	chr11:85434057-85470941	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
23	nsv1051644	chr11:85434057-85471132	Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
24	nsv555637	chr11:85435730-85470893	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
25	nsv555638	chr11:85436303-85458076	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
26	nsv555639	chr11:85436352-85495269	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
27	nsv1048750	chr11:85436840-85471132	Enhancers Genic enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
28	esv2754674	chr11:85436852-85470852	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
29	esv2757459	chr11:85436868-85473347	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
30	nsv541112	chr11:85436956-85468985	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
31	nsv541113	chr11:85437155-85468845	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs540063	ANKRD42	cis	parietal	SCAN
rs540063	SYTL2	cis	Muscle Skeletal	GTEx
rs540063	ME3	cis	cerebellum	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85417600-85453000	Weak transcription	Gastric	stomach
2	chr11:85430400-85459000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr11:85430400-85480400	Weak transcription	Aorta	Aorta
4	chr11:85430800-85459000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr11:85431400-85451600	Weak transcription	HSMMtube	muscle
6	chr11:85431800-85466600	Weak transcription	Brain Substantia Nigra	brain
7	chr11:85432000-85460800	Weak transcription	Fetal Muscle Leg	muscle
8	chr11:85435600-85456400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr11:85436600-85449200	Weak transcription	Small Intestine	intestine
10	chr11:85437600-85451000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr11:85437600-85451600	Weak transcription	Osteobl	bone
12	chr11:85437600-85459800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr11:85437800-85458000	Weak transcription	HSMM	muscle
14	chr11:85439000-85453400	Weak transcription	Colonic Mucosa	Colon
15	chr11:85441400-85456600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr11:85441600-85460200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr11:85442200-85461000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr11:85444400-85461600	Weak transcription	Lung	lung
19	chr11:85445600-85459800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr11:85445600-85460200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr11:85446200-85449800	Weak transcription	NHDF-Ad	bronchial
22	chr11:85447400-85449400	Enhancers	Primary T cells from cord blood	blood
23	chr11:85447400-85449600	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr11:85447400-85459200	Weak transcription	NH-A	brain
25	chr11:85447400-85459400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr11:85447600-85449600	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr11:85447600-85451400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr11:85447600-85459400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr11:85447800-85450200	Enhancers	HUVEC	blood vessel
30	chr11:85448000-85449800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr11:85448000-85451400	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr11:85448000-85463600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr11:85448000-85480600	Weak transcription	Fetal Stomach	stomach
34	chr11:85448200-85449400	Enhancers	Primary T cells fromperipheralblood	blood
35	chr11:85448200-85449400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr11:85448200-85452400	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr11:85448200-85460400	Weak transcription	NHLF	lung
38	chr11:85448400-85449200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr11:85448400-85449400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
40	chr11:85448400-85449800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr11:85448400-85449800	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr11:85448400-85450200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr11:85448400-85451400	Enhancers	Fetal Heart	heart
44	chr11:85448600-85449200	Enhancers	Fetal Intestine Large	intestine
45	chr11:85448600-85449200	Enhancers	Fetal Intestine Small	intestine
46	chr11:85448600-85449200	Enhancers	Fetal Kidney	kidney
47	chr11:85448600-85449200	Enhancers	Fetal Thymus	thymus
48	chr11:85448600-85449200	Enhancers	Placenta Amnion	Placenta Amnion
49	chr11:85448600-85449200	Enhancers	Sigmoid Colon	Sigmoid Colon
50	chr11:85448600-85449200	Enhancers	NHEK	skin

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