Variant report

Variant	rs2508860
Chromosome Location	chr11:71805052-71805053
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:71804181-71805114	GM12892	blood:	n/a	n/a
2	POLR2A	chr11:71803605-71805111	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr11:71804286-71805061	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr11:71804248-71805314	HepG2	liver:	n/a	n/a
5	POLR2A	chr11:71804192-71805097	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr11:71805047-71805072	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:71721753..71723489-chr11:71803888..71805606,2	MCF-7	breast:
2	chr11:71743810..71760160-chr11:71777190..71805714,79	MCF-7	breast:
3	chr11:71791686..71794615-chr11:71803298..71806095,2	MCF-7	breast:

Variant related genes	Relation type
LRTOMT	TF binding region
ENSG00000137497	Chromatin interaction
ENSG00000184154	Chromatin interaction
ENSG00000206783	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10501408	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1057992	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10736780	0.81[ASN][1000 genomes]
rs10736783	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10751188	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10751191	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10751192	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10793011	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10793013	0.81[ASN][1000 genomes]
rs10793014	0.81[ASN][1000 genomes]
rs10793015	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10898812	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11235441	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11235444	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12272086	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12275171	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12293195	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12417471	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1541304	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1548348	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1573501	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1573503	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17161751	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1892920	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1894004	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2155142	0.81[ASN][1000 genomes]
rs2155145	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2155146	0.84[EUR][1000 genomes]
rs2276384	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2276396	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2503	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2508856	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2511120	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2735787	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2845860	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2852365	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3018310	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3750907	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3829215	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4245463	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4378421	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4387373	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4412771	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4477459	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs482197	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4944243	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4945378	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4945392	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs510925	0.86[AMR][1000 genomes]
rs541228	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs56255748	0.81[ASN][1000 genomes]
rs564294	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs567026	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs575831	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs575871	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs577435	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58417942	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs595062	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60054591	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs612255	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs628025	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs645603	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6592447	0.81[ASN][1000 genomes]
rs6592456	0.92[AFR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6592457	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs661290	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs671132	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs674319	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs686340	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7101553	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7102523	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7106653	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7106730	0.81[ASN][1000 genomes]
rs7111379	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7113436	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7113520	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7115513	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7121080	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7126394	0.89[EUR][1000 genomes]
rs73531955	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73543612	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73543635	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73543640	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73543643	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7924834	0.81[ASN][1000 genomes]
rs7942626	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs949326	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9666346	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][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	nsv530623	chr11:71088949-72020418	Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2508860	NUMA1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:71792400-71805200	Weak transcription	HSMMtube	muscle
2	chr11:71792400-71805800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr11:71792600-71805400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr11:71792600-71805400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr11:71792600-71805400	Weak transcription	Colonic Mucosa	Colon
6	chr11:71792600-71805600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr11:71792600-71805600	Weak transcription	Esophagus	oesophagus
8	chr11:71792600-71805600	Weak transcription	Pancreas	Pancrea
9	chr11:71792600-71808800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr11:71792600-71809000	Weak transcription	Psoas Muscle	Psoas
11	chr11:71792600-71812800	Weak transcription	Fetal Heart	heart
12	chr11:71792600-71813200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr11:71792800-71808200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr11:71792800-71808200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr11:71793000-71808400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr11:71793200-71808400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr11:71793400-71805400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr11:71796400-71807600	Weak transcription	HMEC	breast
19	chr11:71797000-71805600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr11:71797400-71808000	Weak transcription	Fetal Kidney	kidney
21	chr11:71798000-71812200	Weak transcription	Fetal Brain Male	brain
22	chr11:71798200-71805600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr11:71800000-71805600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr11:71800200-71805400	Weak transcription	NH-A	brain
25	chr11:71800200-71805600	Weak transcription	Ovary	ovary
26	chr11:71800400-71812000	Strong transcription	Primary T cells from cord blood	blood
27	chr11:71801400-71805600	Weak transcription	NHDF-Ad	bronchial
28	chr11:71801600-71805200	Weak transcription	Spleen	Spleen
29	chr11:71801600-71805400	Weak transcription	Fetal Brain Female	brain
30	chr11:71802200-71805600	Weak transcription	Hela-S3	cervix
31	chr11:71802400-71805600	Weak transcription	HSMM	muscle
32	chr11:71802600-71805600	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr11:71802600-71805600	Weak transcription	Lung	lung
34	chr11:71802800-71805200	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr11:71802800-71805200	Weak transcription	Colon Smooth Muscle	Colon
36	chr11:71802800-71805400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr11:71802800-71805400	Weak transcription	Left Ventricle	heart
38	chr11:71802800-71805600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr11:71802800-71805600	Weak transcription	Stomach Mucosa	stomach
40	chr11:71802800-71808000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr11:71802800-71808000	Weak transcription	Small Intestine	intestine
42	chr11:71802800-71808200	Weak transcription	HepG2	liver
43	chr11:71802800-71809200	Weak transcription	HUVEC	blood vessel
44	chr11:71802800-71810000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr11:71803000-71805200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr11:71803000-71805400	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr11:71803000-71805600	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr11:71803000-71806800	Strong transcription	GM12878-XiMat	blood
49	chr11:71803000-71810800	Strong transcription	Fetal Muscle Leg	muscle
50	chr11:71803200-71805400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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