Variant report

Variant	rs2227292
Chromosome Location	chr3:50608480-50608481
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:50608383-50608893	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr3:50607942-50608680	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr3:50607853-50609897	K562	blood:	n/a	n/a
4	POLR2A	chr3:50607826-50608538	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:50607721-50609802	K562	blood:	n/a	n/a
6	POLR2A	chr3:50608130-50608802	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr3:50607811-50608603	HepG2	liver:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:50608421..50610660-chr3:51421926..51423993,2	K562	blood:
2	chr3:50606526..50611586-chr3:50612274..50616724,6	MCF-7	breast:
3	chr3:50599337..50613537-chr3:50634306..50660129,118	MCF-7	breast:
4	chr3:50607017..50612379-chr3:51423330..51426962,5	MCF-7	breast:
5	chr3:50603678..50606532-chr3:50606738..50608762,2	K562	blood:
6	chr3:50607067..50609858-chr3:50721017..50723839,2	K562	blood:
7	chr3:50608156..50612219-chr3:50612794..50616407,4	K562	blood:
8	chr3:50601756..50613871-chr3:50647072..50654542,28	K562	blood:
9	chr3:50603678..50606671-chr3:50607262..50609999,2	K562	blood:

No data

Variant related genes	Relation type
C3orf18	TF binding region
ENSG00000114735	Chromatin interaction
ENSG00000088543	Chromatin interaction
ENSG00000114737	Chromatin interaction
ENSG00000114738	Chromatin interaction
ENSG00000228337	Chromatin interaction
ENSG00000145050	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1077215	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1107312	0.85[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12486143	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12486717	0.85[ASN][1000 genomes]
rs12487817	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12489607	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12491440	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12491812	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12492093	0.87[ASN][1000 genomes]
rs12492540	0.87[ASN][1000 genomes]
rs12492982	0.88[ASN][1000 genomes]
rs12494094	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12494326	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12494707	0.92[AMR][1000 genomes]
rs12495399	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs17050991	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17050995	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs17051000	0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs17051043	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17051045	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17051403	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs175634	0.81[CHD][hapmap]
rs1872184	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1894459	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2035484	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2076927	0.83[ASN][1000 genomes]
rs2170840	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2227293	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2239750	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2239751	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2239752	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2239753	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2285090	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3749265	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3752449	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792323	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3806706	0.85[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs419160	1.00[YRI][hapmap]
rs4476497	0.90[ASN][1000 genomes]
rs4640555	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4688705	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4688707	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4688709	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688710	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4688713	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4688715	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4688716	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56170012	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs56856095	0.82[ASN][1000 genomes]
rs57910827	0.87[ASN][1000 genomes]
rs58427389	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs58529408	0.80[ASN][1000 genomes]
rs59036236	0.85[ASN][1000 genomes]
rs60552073	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs60877431	0.86[ASN][1000 genomes]
rs61193866	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs61316441	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61574029	0.89[ASN][1000 genomes]
rs61613532	0.90[ASN][1000 genomes]
rs616689	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6446208	0.86[ASN][1000 genomes]
rs650655	0.88[ASN][1000 genomes]
rs6766638	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6771348	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6783922	0.90[ASN][1000 genomes]
rs6794155	0.85[ASN][1000 genomes]
rs728902	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs72938758	0.90[ASN][1000 genomes]
rs72942785	0.87[ASN][1000 genomes]
rs72942794	0.85[ASN][1000 genomes]
rs72944726	0.80[ASN][1000 genomes]
rs72944730	0.80[ASN][1000 genomes]
rs73835531	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs743753	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs745356	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs762889	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808148	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs876103	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs876104	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs876105	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9814874	0.85[CHB][hapmap]
rs9868889	0.90[ASN][1000 genomes]
rs9879397	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
4	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv432419	chr3:50388396-50637496	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv1013225	chr3:50440826-50700448	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv536566	chr3:50440826-50700448	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv984540	chr3:50473691-50669310	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
9	nsv1012501	chr3:50483037-50679591	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
10	nsv536567	chr3:50483037-50679591	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
11	nsv460532	chr3:50536273-50616049	Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases
12	nsv590272	chr3:50536273-50616049	Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases
13	nsv460533	chr3:50574213-50678151	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
14	nsv590273	chr3:50574213-50678151	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
15	esv3423308	chr3:50608207-50608501	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	6 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50607400-50615600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr3:50607400-50628200	Weak transcription	Small Intestine	intestine
3	chr3:50607600-50608600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr3:50607600-50608600	Enhancers	Pancreas	Pancrea
5	chr3:50607600-50609400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:50607600-50609400	Weak transcription	Esophagus	oesophagus
7	chr3:50607600-50609400	Weak transcription	Right Atrium	heart
8	chr3:50607600-50609600	Weak transcription	Spleen	Spleen
9	chr3:50607600-50609800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr3:50607600-50609800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr3:50607600-50609800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr3:50607600-50609800	Weak transcription	Left Ventricle	heart
13	chr3:50607600-50609800	Weak transcription	Lung	lung
14	chr3:50607600-50609800	Weak transcription	Stomach Mucosa	stomach
15	chr3:50607600-50610400	Enhancers	Primary T cells from cord blood	blood
16	chr3:50607600-50613000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr3:50607600-50614400	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr3:50607600-50617600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:50607600-50628400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:50607800-50608600	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr3:50607800-50608600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:50607800-50608600	Enhancers	Placenta	Placenta
23	chr3:50607800-50608600	Enhancers	Gastric	stomach
24	chr3:50607800-50608800	Enhancers	Colon Smooth Muscle	Colon
25	chr3:50607800-50608800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr3:50607800-50609200	Weak transcription	Right Ventricle	heart
27	chr3:50607800-50609600	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr3:50607800-50609800	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr3:50607800-50609800	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr3:50607800-50609800	Enhancers	Fetal Intestine Large	intestine
31	chr3:50607800-50609800	Enhancers	Fetal Thymus	thymus
32	chr3:50607800-50609800	Weak transcription	Psoas Muscle	Psoas
33	chr3:50607800-50609800	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr3:50607800-50610600	Enhancers	Duodenum Mucosa	Duodenum
35	chr3:50607800-50611800	Enhancers	Liver	Liver
36	chr3:50607800-50612000	Weak transcription	Ovary	ovary
37	chr3:50607800-50614200	Weak transcription	Brain Anterior Caudate	brain
38	chr3:50607800-50614800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr3:50607800-50615200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr3:50607800-50615200	Weak transcription	Aorta	Aorta
41	chr3:50607800-50620000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr3:50607800-50628200	Weak transcription	HSMMtube	muscle
43	chr3:50607800-50628600	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr3:50608000-50608600	Enhancers	Fetal Muscle Leg	muscle
45	chr3:50608000-50609400	Enhancers	Stomach Smooth Muscle	stomach
46	chr3:50608000-50609400	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr3:50608000-50609600	Weak transcription	Primary B cells from cord blood	blood
48	chr3:50608000-50609600	Weak transcription	Rectal Smooth Muscle	rectum
49	chr3:50608000-50609800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr3:50608000-50609800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

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