Variant report

Variant	rs73154633
Chromosome Location	chr3:156870059-156870060
allele	C/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	chr3:156868845-156870232	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr3:156868992-156873002	GM12891	blood:	n/a	n/a
3	POLR2A	chr3:156862893-156872946	A549	lung:	n/a	n/a
4	POLR2A	chr3:156869887-156870398	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr3:156868946-156871954	GM12878	blood:	n/a	n/a
6	POLR2A	chr3:156868865-156871888	K562	blood:	n/a	n/a
7	POLR2A	chr3:156861007-156879269	K562	blood:	n/a	n/a
8	POLR2A	chr3:156863231-156878853	HepG2	liver:	n/a	n/a
9	POLR2A	chr3:156869850-156870141	GM12891	blood:	n/a	n/a
10	POLR2A	chr3:156868856-156872754	GM12878	blood:	n/a	n/a
11	POLR2A	chr3:156870038-156870157	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr3:156869894-156870070	K562	blood:	n/a	n/a
13	POLR2A	chr3:156868728-156873222	GM12878	blood:	n/a	n/a
14	POLR2A	chr3:156870003-156870194	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr3:156868964-156871028	IMR90	lung:	n/a	n/a
16	POLR2A	chr3:156868497-156871316	K562	blood:	n/a	n/a
17	POLR2A	chr3:156868831-156872105	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr3:156868403-156871934	Hela-S3	cervix:	n/a	n/a
19	CHD1	chr3:156868741-156879284	IMR90	lung:	n/a	n/a
20	POLR2A	chr3:156863168-156879174	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr3:156867869-156872315	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr3:156869016-156870096	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr3:156869841-156870544	K562	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000201778	TF binding region
CCNL1	TF binding region

Extended variants
information (count: 109 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10936061	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10936062	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10936063	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10936064	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10936065	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10936066	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10936067	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10936068	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10936069	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10936074	0.90[EUR][1000 genomes]
rs12488480	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12489453	0.92[EUR][1000 genomes]
rs12489799	0.93[EUR][1000 genomes]
rs12490836	0.94[EUR][1000 genomes]
rs12492801	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12496051	0.92[EUR][1000 genomes]
rs12496111	0.95[AFR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12497891	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12630209	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12634818	0.95[AFR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12635088	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12636125	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16827318	0.92[EUR][1000 genomes]
rs16827352	0.90[EUR][1000 genomes]
rs17552941	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1995304	0.95[AFR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2321740	0.85[EUR][1000 genomes]
rs35910014	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3935750	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41272613	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4371471	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4383467	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4413278	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4608646	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4679788	0.92[EUR][1000 genomes]
rs4680340	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4680343	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4680345	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4680349	0.82[EUR][1000 genomes]
rs5003893	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55828309	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55835412	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55949516	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55953639	0.95[AFR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56078410	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56263456	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57322659	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57511361	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59210914	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59279023	0.90[EUR][1000 genomes]
rs59485606	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59865540	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60153077	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61149035	0.95[AFR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62274129	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62274155	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62274156	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62274159	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62276460	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62276461	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62276462	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62276465	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62276470	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62276471	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62276474	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62276475	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62276479	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62276480	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62276488	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62276489	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62276490	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62276491	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62276495	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62276496	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62276497	0.90[AFR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62276501	0.93[EUR][1000 genomes]
rs62276502	0.84[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs62276504	0.92[EUR][1000 genomes]
rs62276505	0.90[EUR][1000 genomes]
rs6441115	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6441116	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6441119	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6768052	0.95[AFR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6768074	0.90[EUR][1000 genomes]
rs6777922	0.87[AFR][1000 genomes]
rs6780205	0.90[EUR][1000 genomes]
rs6781682	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6792479	0.95[AFR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6805989	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6806232	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6809307	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73154649	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73154657	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73154659	0.92[EUR][1000 genomes]
rs73154671	0.84[EUR][1000 genomes]
rs73154682	0.82[EUR][1000 genomes]
rs73873800	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7621912	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7626589	0.84[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs7633004	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7648599	0.93[EUR][1000 genomes]
rs7652298	0.82[EUR][1000 genomes]
rs8180056	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8180057	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8925	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	esv3349885	chr3:156685409-156878910	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
2	nsv829766	chr3:156811536-157020551	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv520331	chr3:156858300-156915650	Flanking Active TSS Active TSS Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
4	nsv819788	chr3:156869993-156871291	Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156848600-156876600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:156852600-156873400	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr3:156853400-156872000	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr3:156855000-156872000	Weak transcription	Right Atrium	heart
5	chr3:156855400-156877000	Weak transcription	Gastric	stomach
6	chr3:156856000-156870800	Strong transcription	Primary T cells from cord blood	blood
7	chr3:156856000-156874600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr3:156858000-156871200	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr3:156858000-156872000	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr3:156858200-156870400	Strong transcription	Liver	Liver
11	chr3:156858200-156871200	Strong transcription	Adipose Nuclei	Adipose
12	chr3:156858400-156876400	Strong transcription	Fetal Muscle Trunk	muscle
13	chr3:156858600-156871200	Strong transcription	Duodenum Mucosa	Duodenum
14	chr3:156858600-156871200	Strong transcription	Stomach Smooth Muscle	stomach
15	chr3:156858600-156872200	Strong transcription	Primary B cells from cord blood	blood
16	chr3:156858600-156872400	Strong transcription	Sigmoid Colon	Sigmoid Colon
17	chr3:156859000-156871800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr3:156859200-156870800	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr3:156859400-156872200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:156859400-156872400	Strong transcription	Primary B cells from peripheral blood	blood
21	chr3:156859400-156876200	Strong transcription	Placenta	Placenta
22	chr3:156859800-156871600	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr3:156859800-156871800	Strong transcription	Fetal Muscle Leg	muscle
24	chr3:156860000-156871000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr3:156860000-156871000	Strong transcription	Brain Substantia Nigra	brain
26	chr3:156860000-156871200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr3:156860000-156872000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:156860000-156872200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:156860000-156872200	Strong transcription	A549	lung
30	chr3:156860000-156872400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr3:156860000-156872400	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr3:156860000-156872800	Strong transcription	HSMM	muscle
33	chr3:156860000-156874000	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr3:156860200-156871200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr3:156860200-156871400	Strong transcription	Colon Smooth Muscle	Colon
36	chr3:156860200-156872400	Strong transcription	Fetal Brain Female	brain
37	chr3:156860800-156871800	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr3:156860800-156872200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr3:156860800-156872400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr3:156860800-156872400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr3:156860800-156872600	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr3:156861000-156870800	Strong transcription	Dnd41	blood
43	chr3:156861000-156871200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr3:156861000-156871200	Strong transcription	Brain Inferior Temporal Lobe	brain
45	chr3:156861000-156871400	Strong transcription	Fetal Lung	lung
46	chr3:156861000-156871600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:156861000-156872000	Strong transcription	HUVEC	blood vessel
48	chr3:156861200-156871600	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr3:156861200-156871600	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr3:156861200-156872000	Strong transcription	NHDF-Ad	bronchial

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