Variant report

Variant	rs948561
Chromosome Location	chr11:58407766-58407767
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:58385876..58387982-chr11:58406021..58408836,2	MCF-7	breast:
2	chr11:58344813..58346955-chr11:58405857..58408185,2	MCF-7	breast:
3	chr11:58402145..58403700-chr11:58406157..58408220,2	K562	blood:
4	chr11:58405749..58408727-chr11:58417141..58419096,2	K562	blood:
5	chr11:58402930..58405768-chr11:58406418..58410060,3	K562	blood:

Variant related genes	Relation type
ENSG00000255073	Chromatin interaction
ENSG00000110031	Chromatin interaction
ENSG00000186660	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs1009171	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1009172	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1009173	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1047979	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10792173	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10792174	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10792175	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10792176	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10792177	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10792178	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10792179	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10896791	0.83[ASN][1000 genomes]
rs10896792	0.83[ASN][1000 genomes]
rs10896798	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10896799	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10896800	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10896801	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10896802	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10896803	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10896804	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10896805	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10896806	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10896807	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10896808	0.88[ASN][1000 genomes]
rs10896809	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10896810	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10896811	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10896812	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11229518	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11229527	0.83[ASN][1000 genomes]
rs11229551	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11229553	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11229554	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11229556	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11229557	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11229558	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11229559	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11229560	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11229561	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11229563	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11229565	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11229568	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11229569	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11522717	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11604156	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11605641	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11607534	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12361824	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12362218	0.83[ASN][1000 genomes]
rs12785991	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17490208	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17490375	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1938596	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1938599	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1938600	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1938602	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1938604	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1938605	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1938606	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1938607	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1938608	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1938610	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1938611	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1938612	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1941966	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1941967	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1941968	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1944050	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1944054	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1954694	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1954871	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2154630	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2154631	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2154632	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2245938	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2276151	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2507758	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2507763	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2509914	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2509915	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2509916	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2509919	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2509920	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2509924	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2509928	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2510552	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2510557	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2510559	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2515343	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2515346	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2515347	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2515352	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2515353	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2515354	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2515357	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2515359	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2515362	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2515363	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2515364	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3133439	0.81[ASN][1000 genomes]
rs3133440	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4319530	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59104317	0.83[ASN][1000 genomes]
rs61889553	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6591483	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7127513	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7350490	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7926718	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7940789	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7941135	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7942923	0.82[ASN][1000 genomes]
rs7948312	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs948560	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9888176	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832168	chr11:58394060-58564651	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1050013	chr11:58394598-59221090	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv1050444	chr11:58404467-58434568	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58393800-58407800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr11:58394000-58407800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr11:58394800-58408200	Weak transcription	Duodenum Mucosa	Duodenum
4	chr11:58395800-58407800	Weak transcription	Fetal Thymus	thymus
5	chr11:58402400-58407800	Weak transcription	Fetal Intestine Small	intestine
6	chr11:58404400-58408000	Weak transcription	Ovary	ovary
7	chr11:58405200-58407800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr11:58406000-58410200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr11:58406200-58408200	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr11:58406200-58411200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr11:58406200-58413000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr11:58406600-58409200	Enhancers	Brain Hippocampus Middle	brain
13	chr11:58406800-58409000	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr11:58407000-58408200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr11:58407000-58408400	Enhancers	Brain Anterior Caudate	brain
16	chr11:58407000-58408800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr11:58407000-58408800	Enhancers	Brain Angular Gyrus	brain
18	chr11:58407000-58408800	Enhancers	Thymus	Thymus
19	chr11:58407000-58409000	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr11:58407000-58409000	Enhancers	Primary T cells fromperipheralblood	blood
21	chr11:58407000-58409000	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr11:58407000-58409000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr11:58407000-58409000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr11:58407000-58409200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr11:58407200-58407800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr11:58407200-58408400	Enhancers	Primary T cells from cord blood	blood
27	chr11:58407200-58408600	Enhancers	Left Ventricle	heart
28	chr11:58407200-58408600	Enhancers	Lung	lung
29	chr11:58407200-58408800	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr11:58407200-58408800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr11:58407200-58408800	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr11:58407200-58408800	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr11:58407200-58408800	Enhancers	Spleen	Spleen
34	chr11:58407200-58408800	Enhancers	Dnd41	blood
35	chr11:58407200-58409200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr11:58407200-58409600	Enhancers	Primary hematopoietic stem cells	blood
37	chr11:58407200-58410000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr11:58407400-58408400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr11:58407400-58408600	Enhancers	Adipose Nuclei	Adipose
40	chr11:58407400-58408800	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr11:58407400-58408800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr11:58407400-58408800	Enhancers	Brain Cingulate Gyrus	brain
43	chr11:58407400-58408800	Enhancers	Brain Substantia Nigra	brain
44	chr11:58407400-58409000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr11:58407600-58408400	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr11:58407600-58408400	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr11:58407600-58408600	Enhancers	Primary B cells from peripheral blood	blood
48	chr11:58407600-58408600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr11:58407600-58408600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
50	chr11:58407600-58408600	Enhancers	Monocytes-CD14+_RO01746	blood

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