Variant report

Variant	rs6441119
Chromosome Location	chr3:156894764-156894765
allele	G/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	chr3:156894648-156894764	MCF10A-Er-Src	breast:	n/a	n/a
2	MXI1	chr3:156891834-156895033	IMR90	lung:	n/a	n/a
3	MXI1	chr3:156891521-156894953	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:156347077..156349787-chr3:156893431..156895606,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCNL1-4	chr3:156894242-156894786	NONHSAT092909

Variant related genes	Relation type
RNA5SP146	TF binding region

Extended variants
information (count: 114 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10936061	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936062	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936063	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936064	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936065	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936066	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936067	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10936068	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10936069	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10936074	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10936075	0.82[EUR][1000 genomes]
rs1157738	0.84[AMR][1000 genomes]
rs12488480	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12489453	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12489799	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12490836	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12492801	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12496051	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12496111	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12497891	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12630209	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12633429	0.82[EUR][1000 genomes]
rs12634818	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12635088	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12636125	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16827318	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16827322	0.84[AMR][1000 genomes]
rs16827352	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17552941	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1995304	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2321740	0.88[EUR][1000 genomes]
rs35910014	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3935750	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41272613	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4371471	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4383467	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4413278	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4608646	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679788	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4680340	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4680343	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680345	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680347	0.84[AMR][1000 genomes]
rs4680349	0.85[EUR][1000 genomes]
rs5003893	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55828309	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55835412	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55949516	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55953639	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56078410	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56263456	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57322659	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57511361	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59210914	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59279023	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59485606	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59865540	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60153077	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61149035	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62274129	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62274155	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62274156	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62274159	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62276460	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62276461	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62276462	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62276465	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62276470	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62276471	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62276474	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62276475	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62276479	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62276480	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62276488	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62276489	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62276490	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62276491	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62276495	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62276496	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62276497	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62276501	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62276502	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62276504	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62276505	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6441115	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441116	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6768052	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6768074	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6777922	0.87[AFR][1000 genomes]
rs6780205	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6781682	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792479	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6805989	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6806232	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6809307	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73154633	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73154649	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73154657	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73154659	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73154671	0.86[EUR][1000 genomes]
rs73154682	0.84[EUR][1000 genomes]
rs73873800	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7610214	0.82[EUR][1000 genomes]
rs7621912	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626589	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7633004	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7648599	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7652298	0.84[EUR][1000 genomes]
rs8180056	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8180057	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8925	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs949854	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156892400-156895000	Active TSS	GM12878-XiMat	blood
2	chr3:156893800-156894800	Enhancers	Placenta Amnion	Placenta Amnion
3	chr3:156893800-156894800	Flanking Active TSS	Dnd41	blood
4	chr3:156893800-156895200	Enhancers	Spleen	Spleen
5	chr3:156894000-156895200	Enhancers	Primary B cells from peripheral blood	blood
6	chr3:156894000-156895200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr3:156894000-156900800	Weak transcription	Ovary	ovary
8	chr3:156894200-156894800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:156894200-156894800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
10	chr3:156894200-156894800	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr3:156894200-156894800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr3:156894200-156894800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr3:156894200-156894800	Enhancers	Thymus	Thymus
14	chr3:156894200-156895000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:156894200-156895000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:156894200-156895000	Enhancers	Primary B cells from cord blood	blood
17	chr3:156894200-156895000	Enhancers	Fetal Muscle Trunk	muscle
18	chr3:156894200-156895000	Enhancers	Fetal Muscle Leg	muscle
19	chr3:156894200-156895200	Enhancers	Primary T cells fromperipheralblood	blood
20	chr3:156894200-156895200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr3:156894200-156895600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr3:156894200-156895600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
23	chr3:156894200-156896200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:156894200-156896200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:156894200-156896200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr3:156894200-156896200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr3:156894200-156896200	Weak transcription	Colonic Mucosa	Colon
28	chr3:156894200-156896200	Weak transcription	Fetal Stomach	stomach
29	chr3:156894200-156901600	Weak transcription	Right Atrium	heart
30	chr3:156894200-156903000	Weak transcription	Esophagus	oesophagus
31	chr3:156894400-156894800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:156894400-156894800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr3:156894400-156894800	Active TSS	Fetal Brain Male	brain
34	chr3:156894400-156894800	Enhancers	Fetal Intestine Small	intestine
35	chr3:156894400-156894800	Enhancers	Fetal Thymus	thymus
36	chr3:156894400-156894800	Weak transcription	Left Ventricle	heart
37	chr3:156894400-156894800	Weak transcription	Lung	lung
38	chr3:156894400-156894800	Weak transcription	Pancreas	Pancrea
39	chr3:156894400-156894800	Enhancers	Hela-S3	cervix
40	chr3:156894400-156894800	Flanking Active TSS	K562	blood
41	chr3:156894400-156895000	Enhancers	Primary hematopoietic stem cells	blood
42	chr3:156894400-156895000	Enhancers	Brain Substantia Nigra	brain
43	chr3:156894400-156895200	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr3:156894400-156895200	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr3:156894400-156895200	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr3:156894400-156895200	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr3:156894400-156895200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr3:156894400-156895200	Enhancers	Fetal Intestine Large	intestine
49	chr3:156894400-156895400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr3:156894400-156895400	Enhancers	Primary T killer memory cells from peripheral blood	blood

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