Variant report

Variant	rs11065254
Chromosome Location	chr12:121198392-121198393
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:121197854..121198510-chr12:121441406..121442179,2	MCF-7	breast:

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1055059	1.00[ASN][1000 genomes]
rs10849777	0.82[CEU][hapmap];1.00[ASN][1000 genomes]
rs10849797	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065179	1.00[ASN][1000 genomes]
rs11065201	1.00[ASN][1000 genomes]
rs11065207	1.00[ASN][1000 genomes]
rs11065208	0.82[CEU][hapmap]
rs11065210	1.00[ASN][1000 genomes]
rs11065213	0.82[CEU][hapmap];1.00[ASN][1000 genomes]
rs11065226	1.00[ASN][1000 genomes]
rs11065227	1.00[ASN][1000 genomes]
rs11065228	1.00[ASN][1000 genomes]
rs11065253	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065258	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065260	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065263	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11065267	0.82[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065275	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065279	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065281	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11065285	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065288	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065291	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065294	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065308	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11065309	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11065315	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11065318	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11065326	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11065328	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11065334	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11065347	1.00[ASN][1000 genomes]
rs11065353	1.00[ASN][1000 genomes]
rs1151854	1.00[ASN][1000 genomes]
rs1151855	1.00[ASN][1000 genomes]
rs1151860	1.00[ASN][1000 genomes]
rs1151865	0.82[CEU][hapmap];1.00[ASN][1000 genomes]
rs1186042	1.00[ASN][1000 genomes]
rs12366451	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12368617	1.00[ASN][1000 genomes]
rs12370534	1.00[ASN][1000 genomes]
rs1696358	1.00[ASN][1000 genomes]
rs1718207	1.00[ASN][1000 genomes]
rs1732397	1.00[ASN][1000 genomes]
rs1732399	1.00[ASN][1000 genomes]
rs2454728	1.00[ASN][1000 genomes]
rs2701179	1.00[ASN][1000 genomes]
rs497457	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs498255	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs513940	1.00[ASN][1000 genomes]
rs515784	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs519785	0.82[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs530162	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs554197	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs572009	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs574993	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs581197	1.00[ASN][1000 genomes]
rs581515	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs582678	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs590556	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs591489	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59818945	1.00[ASN][1000 genomes]
rs61108232	1.00[ASN][1000 genomes]
rs61414515	1.00[ASN][1000 genomes]
rs61624288	1.00[ASN][1000 genomes]
rs627211	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs639343	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs645661	1.00[ASN][1000 genomes]
rs645786	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs647336	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs648262	1.00[ASN][1000 genomes]
rs651156	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs660878	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs671815	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs708784	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs708788	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73409953	1.00[ASN][1000 genomes]
rs73411916	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73413866	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73413874	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7960932	1.00[ASN][1000 genomes]
rs949443	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1041153	chr12:121171986-121208826	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv560438	chr12:121194565-121352206	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121186400-121198400	Weak transcription	Right Ventricle	heart
2	chr12:121193000-121198400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr12:121194000-121200800	Weak transcription	HepG2	liver
4	chr12:121194200-121202200	Weak transcription	K562	blood
5	chr12:121194800-121198800	Weak transcription	A549	lung
6	chr12:121195000-121201200	Weak transcription	Small Intestine	intestine
7	chr12:121195200-121200000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr12:121195400-121198400	Weak transcription	Dnd41	blood
9	chr12:121195400-121198800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr12:121195600-121198400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr12:121195600-121198600	Weak transcription	Colonic Mucosa	Colon
12	chr12:121195600-121198800	Weak transcription	NHLF	lung
13	chr12:121195600-121199200	Weak transcription	NHDF-Ad	bronchial
14	chr12:121195600-121204200	Weak transcription	Stomach Mucosa	stomach
15	chr12:121195600-121207200	Strong transcription	Brain Germinal Matrix	brain
16	chr12:121196000-121198400	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr12:121196000-121198600	Weak transcription	Brain Angular Gyrus	brain
18	chr12:121196000-121201000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr12:121196200-121199200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr12:121196200-121199400	Weak transcription	Aorta	Aorta
21	chr12:121196200-121201000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr12:121196200-121201000	Weak transcription	Osteobl	bone
23	chr12:121196400-121198600	Weak transcription	Colon Smooth Muscle	Colon
24	chr12:121196400-121198600	Weak transcription	HSMMtube	muscle
25	chr12:121196400-121199000	Weak transcription	HMEC	breast
26	chr12:121196400-121207000	Strong transcription	Fetal Brain Female	brain
27	chr12:121196600-121199000	Weak transcription	Hela-S3	cervix
28	chr12:121196800-121198400	Weak transcription	Primary B cells from cord blood	blood
29	chr12:121196800-121199000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr12:121196800-121199000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr12:121196800-121200200	Enhancers	Psoas Muscle	Psoas
32	chr12:121196800-121201400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr12:121196800-121203000	Strong transcription	Fetal Intestine Large	intestine
34	chr12:121196800-121212800	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr12:121197000-121198600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr12:121197000-121198600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr12:121197000-121198600	Weak transcription	HUVEC	blood vessel
38	chr12:121197000-121199400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr12:121197000-121200200	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr12:121197000-121203000	Strong transcription	Fetal Intestine Small	intestine
41	chr12:121197000-121207200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr12:121197200-121199000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr12:121197200-121199200	Weak transcription	NH-A	brain
44	chr12:121197200-121200800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr12:121197200-121201200	Weak transcription	Ovary	ovary
46	chr12:121197200-121204200	Weak transcription	Fetal Brain Male	brain
47	chr12:121197200-121210000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr12:121197400-121198400	Strong transcription	Stomach Smooth Muscle	stomach
49	chr12:121197400-121198600	Weak transcription	Brain Substantia Nigra	brain
50	chr12:121197400-121198800	Strong transcription	Brain Hippocampus Middle	brain

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