Variant report

Variant	rs41340150
Chromosome Location	chr11:59407512-59407513
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:59406586..59408935-chr11:59435873..59437866,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166889	Chromatin interaction
ENSG00000255355	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10501380	1.00[CHB][hapmap]
rs11230020	1.00[CHB][hapmap];0.91[MEX][hapmap]
rs11230037	1.00[CHB][hapmap];0.90[MEX][hapmap]
rs1151063	1.00[CHB][hapmap];1.00[MEX][hapmap]
rs1151064	1.00[CHB][hapmap];1.00[MEX][hapmap]
rs11821465	1.00[CHB][hapmap];0.91[MEX][hapmap]
rs12278910	0.91[MEX][hapmap]
rs12280606	1.00[CHB][hapmap]
rs12289921	0.91[MEX][hapmap]
rs12292682	1.00[CHB][hapmap]
rs1287111	1.00[CHB][hapmap];1.00[MEX][hapmap]
rs1299800	0.84[JPT][hapmap]
rs1453543	0.90[MEX][hapmap]
rs1530995	1.00[ASW][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap]
rs17153732	0.80[MEX][hapmap]
rs17153766	0.90[MEX][hapmap]
rs17153910	0.91[MEX][hapmap]
rs17153962	1.00[ASW][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap];0.82[ASN][1000 genomes]
rs17153966	0.82[ASN][1000 genomes]
rs17153982	1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[ASN][1000 genomes]
rs17154025	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs17154134	1.00[CHB][hapmap]
rs17154142	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17154146	1.00[CHB][hapmap]
rs17154165	1.00[CHB][hapmap]
rs17154180	1.00[CHB][hapmap]
rs17154200	1.00[CHB][hapmap]
rs17154203	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17154205	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17154216	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17154227	1.00[CHB][hapmap]
rs17596862	1.00[CHB][hapmap]
rs1938690	1.00[CHB][hapmap];0.91[MEX][hapmap]
rs2298589	1.00[JPT][hapmap]
rs2298868	1.00[JPT][hapmap]
rs2298869	1.00[JPT][hapmap]
rs2508335	1.00[CHB][hapmap]
rs2509274	1.00[CHB][hapmap];1.00[MEX][hapmap]
rs2509275	1.00[CHB][hapmap];0.82[MEX][hapmap]
rs2509279	1.00[CHB][hapmap]
rs2509290	1.00[CHB][hapmap]
rs2509730	1.00[CHB][hapmap]
rs2924493	0.81[ASN][1000 genomes]
rs2927184	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs35770960	0.82[ASN][1000 genomes]
rs3781792	1.00[CHB][hapmap]
rs41384548	1.00[CHB][hapmap]
rs4356243	1.00[CHB][hapmap]
rs4393334	1.00[CHB][hapmap]
rs472177	1.00[CHB][hapmap];0.91[MEX][hapmap]
rs473979	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs475145	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs478167	1.00[CHB][hapmap]
rs482355	1.00[CHB][hapmap];1.00[MEX][hapmap]
rs482356	1.00[CHB][hapmap]
rs485803	1.00[CHB][hapmap]
rs486952	1.00[ASW][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap];0.82[ASN][1000 genomes]
rs488331	0.82[MEX][hapmap]
rs495564	0.91[MEX][hapmap]
rs498099	1.00[CHB][hapmap];1.00[MEX][hapmap]
rs499037	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.80[YRI][hapmap]
rs504016	1.00[CHB][hapmap]
rs506384	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap]
rs508411	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs512194	1.00[CHB][hapmap];1.00[MEX][hapmap]
rs513979	1.00[CHB][hapmap]
rs516912	1.00[CHB][hapmap]
rs518026	1.00[JPT][hapmap];0.88[YRI][hapmap]
rs519535	0.82[ASN][1000 genomes]
rs519605	1.00[CHB][hapmap]
rs520622	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs523016	1.00[CHB][hapmap];1.00[MEX][hapmap]
rs524102	1.00[CHB][hapmap]
rs528525	1.00[CHB][hapmap]
rs529270	1.00[CHB][hapmap];1.00[MEX][hapmap]
rs533166	1.00[CHB][hapmap];1.00[MEX][hapmap]
rs536544	1.00[CHB][hapmap];1.00[MEX][hapmap]
rs536910	0.85[JPT][hapmap]
rs537595	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs540684	1.00[CHB][hapmap];1.00[MEX][hapmap]
rs549086	1.00[CHB][hapmap];1.00[MEX][hapmap]
rs552601	1.00[CHB][hapmap];1.00[MEX][hapmap]
rs554848	1.00[CHB][hapmap]
rs555251	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap]
rs559150	1.00[ASW][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap];0.82[ASN][1000 genomes]
rs565482	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs567994	0.91[MEX][hapmap]
rs573592	1.00[CHB][hapmap]
rs577224	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs579373	1.00[CHB][hapmap];1.00[MEX][hapmap]
rs60146927	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6591541	0.91[MEX][hapmap]
rs693110	0.82[JPT][hapmap]
rs7119778	1.00[CHB][hapmap]
rs7123969	1.00[CHB][hapmap]
rs7126593	1.00[CHB][hapmap]
rs7131059	1.00[CHB][hapmap]
rs73488804	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7937245	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7937684	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7939527	1.00[JPT][hapmap];0.85[YRI][hapmap]
rs7947036	1.00[CHB][hapmap]
rs7947514	1.00[CHB][hapmap]
rs7952024	1.00[CHB][hapmap]
rs7952495	1.00[JPT][hapmap];0.82[YRI][hapmap]
rs8280	0.91[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1797571	chr11:59383323-59424688	Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	esv1797737	chr11:59383323-59424688	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	esv1802782	chr11:59383323-59448068	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv832172	chr11:59396407-59431115	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	esv3343702	chr11:59407503-59407988	Strong transcription Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:59393600-59408200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:59395600-59409800	Weak transcription	Fetal Heart	heart
3	chr11:59395600-59434600	Weak transcription	Stomach Mucosa	stomach
4	chr11:59402200-59411800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr11:59402200-59427000	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr11:59402200-59432400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr11:59402200-59434000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr11:59402400-59408600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr11:59402400-59427800	Strong transcription	Muscle Satellite Cultured Cells	--
10	chr11:59402400-59428200	Strong transcription	Primary T cells from cord blood	blood
11	chr11:59402600-59408600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr11:59402600-59409200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr11:59402600-59410600	Strong transcription	Skeletal Muscle Male	skeletal muscle
14	chr11:59402600-59410800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr11:59402600-59410800	Strong transcription	Liver	Liver
16	chr11:59402600-59411200	Strong transcription	Fetal Stomach	stomach
17	chr11:59402600-59411200	Strong transcription	Spleen	Spleen
18	chr11:59402600-59424200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr11:59402600-59426800	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr11:59402600-59427200	Strong transcription	Primary hematopoietic stem cells	blood
21	chr11:59402600-59427400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr11:59402600-59427600	Strong transcription	Adipose Nuclei	Adipose
23	chr11:59402600-59427600	Strong transcription	GM12878-XiMat	blood
24	chr11:59402600-59428000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr11:59402600-59428000	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr11:59402600-59428400	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr11:59402600-59428400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr11:59402600-59428600	Strong transcription	Fetal Muscle Leg	muscle
29	chr11:59402600-59429000	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr11:59402600-59434000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr11:59402600-59434000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr11:59402600-59434200	Strong transcription	Fetal Muscle Trunk	muscle
33	chr11:59402600-59434400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr11:59402800-59408600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr11:59402800-59410600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr11:59402800-59410800	Strong transcription	Stomach Smooth Muscle	stomach
37	chr11:59402800-59411200	Strong transcription	Fetal Intestine Small	intestine
38	chr11:59402800-59411200	Strong transcription	Lung	lung
39	chr11:59402800-59411400	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr11:59402800-59413200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr11:59402800-59426600	Strong transcription	Primary B cells from peripheral blood	blood
42	chr11:59402800-59427000	Strong transcription	Ovary	ovary
43	chr11:59402800-59427200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr11:59402800-59427200	Strong transcription	HUVEC	blood vessel
45	chr11:59402800-59428000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr11:59402800-59428000	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr11:59402800-59428000	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr11:59402800-59428000	Strong transcription	Placenta	Placenta
49	chr11:59402800-59428400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr11:59402800-59428600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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