Variant report

Variant	rs542752
Chromosome Location	chr11:71810644-71810645
allele	A/T
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	chr11:71810555-71810981	K562	blood:	n/a	n/a
2	POLR2A	chr11:71809204-71810987	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr11:71810296-71810775	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr11:71810584-71811806	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr11:71810350-71811600	HepG2	liver:	n/a	n/a
6	POLR2A	chr11:71808442-71812800	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr11:71810539-71811462	K562	blood:	n/a	n/a
8	POLR2A	chr11:71809272-71811065	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:71791097..71793532-chr11:71809805..71812079,4	MCF-7	breast:
2	chr11:71789323..71798359-chr11:71810049..71815293,14	MCF-7	breast:
3	chr11:71808840..71811674-chr11:71882236..71884134,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000238768	TF binding region
LAMTOR1	TF binding region
ENSG00000212089	Chromatin interaction
ENSG00000255860	Chromatin interaction
ENSG00000137497	Chromatin interaction
ENSG00000184154	Chromatin interaction

Extended variants
information (count: 127 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs10128658	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10736786	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10751190	0.85[EUR][1000 genomes]
rs10751193	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10793016	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10898814	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10898817	0.80[ASN][1000 genomes]
rs11235440	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12272213	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12283462	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12293885	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1541306	0.83[EUR][1000 genomes]
rs1573500	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1573502	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17161966	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17161980	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17161991	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1791544	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1806778	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1892919	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1892921	0.85[EUR][1000 genomes]
rs1894003	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1939242	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1939243	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1939245	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1939247	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2250866	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2298456	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2511074	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2511075	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2511076	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2511078	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2511079	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2511114	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2511116	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2511121	0.84[ASN][1000 genomes]
rs2511122	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2845857	0.90[EUR][1000 genomes]
rs28504107	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3018301	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3018304	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3018308	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3133230	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3133233	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3750908	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3793938	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3814721	0.85[EUR][1000 genomes]
rs3886589	0.81[EUR][1000 genomes]
rs4121395	0.81[EUR][1000 genomes]
rs4338555	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4479013	0.81[EUR][1000 genomes]
rs482013	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs493065	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4943821	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4944242	0.81[EUR][1000 genomes]
rs4944258	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4944259	0.85[ASN][1000 genomes]
rs4945426	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4945434	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4945435	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs495567	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs510925	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs517837	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs541022	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs547208	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs548961	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs552966	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs560777	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56097487	0.83[EUR][1000 genomes]
rs57025151	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs585228	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58991229	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs597513	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs598835	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs607446	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs610004	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs610041	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs615000	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs627329	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs636946	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs642573	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs642618	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs656640	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6592448	0.81[EUR][1000 genomes]
rs6592449	0.81[EUR][1000 genomes]
rs6592451	0.81[EUR][1000 genomes]
rs6592453	0.85[EUR][1000 genomes]
rs6592455	0.85[EUR][1000 genomes]
rs6592458	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6592459	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs659513	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs670802	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs671681	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs673478	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs675185	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs676721	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs677279	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs678193	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs679926	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7101701	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7113549	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7116188	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7116495	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7121260	0.85[EUR][1000 genomes]
rs7123102	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7124000	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7126838	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7127865	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7128317	0.85[EUR][1000 genomes]
rs7128974	0.85[EUR][1000 genomes]
rs73531952	0.85[EUR][1000 genomes]
rs73539529	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73539532	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73543609	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73543633	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7480015	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7924516	0.81[EUR][1000 genomes]
rs7930142	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7930544	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7930721	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7930722	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7937515	0.87[ASN][1000 genomes]
rs7937582	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7949480	0.85[EUR][1000 genomes]
rs947932	0.81[EUR][1000 genomes]
rs949325	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[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
rs542752	NUMA1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:71792600-71812800	Weak transcription	Fetal Heart	heart
2	chr11:71792600-71813200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:71798000-71812200	Weak transcription	Fetal Brain Male	brain
4	chr11:71800400-71812000	Strong transcription	Primary T cells from cord blood	blood
5	chr11:71803000-71810800	Strong transcription	Fetal Muscle Leg	muscle
6	chr11:71803800-71810800	Strong transcription	Rectal Mucosa Donor 29	rectum
7	chr11:71803800-71811200	Strong transcription	Brain Angular Gyrus	brain
8	chr11:71804000-71812800	Strong transcription	Fetal Stomach	stomach
9	chr11:71804200-71811200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr11:71804200-71811600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr11:71804200-71811600	Strong transcription	Gastric	stomach
12	chr11:71804200-71811800	Strong transcription	Brain Inferior Temporal Lobe	brain
13	chr11:71804200-71812200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:71804200-71812200	Strong transcription	Fetal Intestine Large	intestine
15	chr11:71804400-71811000	Strong transcription	Primary B cells from peripheral blood	blood
16	chr11:71804400-71811000	Strong transcription	Rectal Mucosa Donor 31	rectum
17	chr11:71804400-71811200	Strong transcription	Duodenum Mucosa	Duodenum
18	chr11:71804400-71811200	Strong transcription	Fetal Intestine Small	intestine
19	chr11:71804400-71811200	Strong transcription	Osteobl	bone
20	chr11:71804400-71811400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr11:71804400-71811400	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr11:71804400-71811800	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr11:71804400-71811800	Strong transcription	NHLF	lung
24	chr11:71804400-71812800	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr11:71804400-71812800	Strong transcription	A549	lung
26	chr11:71804600-71811600	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr11:71804600-71811800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr11:71804600-71812600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr11:71804800-71811600	Strong transcription	Thymus	Thymus
30	chr11:71804800-71812000	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr11:71805200-71810800	Strong transcription	Spleen	Spleen
32	chr11:71805400-71811200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr11:71805400-71811200	Strong transcription	Colonic Mucosa	Colon
34	chr11:71805600-71810800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr11:71805600-71810800	Strong transcription	Lung	lung
36	chr11:71805600-71811800	Strong transcription	HSMM	muscle
37	chr11:71807400-71811400	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr11:71807400-71812200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr11:71807400-71812400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr11:71807600-71810800	Strong transcription	Brain Anterior Caudate	brain
41	chr11:71807600-71810800	Strong transcription	Brain Cingulate Gyrus	brain
42	chr11:71807600-71810800	Strong transcription	HMEC	breast
43	chr11:71807600-71811200	Strong transcription	Dnd41	blood
44	chr11:71807600-71811200	Strong transcription	Hela-S3	cervix
45	chr11:71807600-71812800	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr11:71807800-71810800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr11:71807800-71812200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr11:71808000-71810800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr11:71808000-71810800	Strong transcription	Fetal Brain Female	brain
50	chr11:71808000-71811200	Weak transcription	Right Atrium	heart

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