Variant report

Variant	rs3885657
Chromosome Location	chr1:223997823-223997824
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:223984690..223986233-chr1:223997368..223999252,2	MCF-7	breast:
2	chr1:223961408..223964143-chr1:223997434..223999357,2	K562	blood:
3	chr1:223902286..223903884-chr1:223996819..223998348,2	K562	blood:
4	chr1:223996924..223999488-chr1:224013619..224016600,2	K562	blood:
5	chr1:223992025..223993711-chr1:223996774..223998979,2	K562	blood:
6	chr1:223995561..223997893-chr1:224022146..224025073,2	K562	blood:

Variant related genes	Relation type
ENSG00000143514	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10159015	0.82[EUR][1000 genomes]
rs10465524	0.82[EUR][1000 genomes]
rs10503144	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10915702	0.81[EUR][1000 genomes]
rs10915707	0.83[EUR][1000 genomes]
rs10915715	0.86[EUR][1000 genomes]
rs1153958	0.82[EUR][1000 genomes]
rs1153965	0.93[EUR][1000 genomes]
rs12046297	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12059128	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12059770	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12060361	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12066704	0.81[EUR][1000 genomes]
rs12066829	0.81[EUR][1000 genomes]
rs12066831	0.81[EUR][1000 genomes]
rs12069561	0.83[EUR][1000 genomes]
rs12070057	0.81[EUR][1000 genomes]
rs12080250	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12088254	0.99[EUR][1000 genomes]
rs12091841	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1222134	0.83[EUR][1000 genomes]
rs1222138	0.82[EUR][1000 genomes]
rs1222140	0.81[EUR][1000 genomes]
rs1222141	0.81[EUR][1000 genomes]
rs12562109	0.83[EUR][1000 genomes]
rs12563291	0.89[EUR][1000 genomes]
rs12563477	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12563637	0.86[EUR][1000 genomes]
rs12563713	0.90[EUR][1000 genomes]
rs12564557	1.00[ASN][1000 genomes]
rs12565202	1.00[ASN][1000 genomes]
rs12565573	1.00[ASN][1000 genomes]
rs12565967	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12566817	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16841190	1.00[ASN][1000 genomes]
rs16842162	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16842229	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16842257	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16842326	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16842343	1.00[ASN][1000 genomes]
rs17597	0.89[EUR][1000 genomes]
rs17598	0.83[EUR][1000 genomes]
rs17600	0.83[EUR][1000 genomes]
rs28370069	0.87[EUR][1000 genomes]
rs28370073	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28370074	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28370088	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28370159	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28370170	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34683843	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36032024	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3738373	0.83[EUR][1000 genomes]
rs3738374	0.83[EUR][1000 genomes]
rs3738375	0.83[EUR][1000 genomes]
rs3767716	0.85[EUR][1000 genomes]
rs3767717	0.83[EUR][1000 genomes]
rs3767718	0.83[EUR][1000 genomes]
rs41303996	1.00[ASN][1000 genomes]
rs58774026	1.00[ASN][1000 genomes]
rs59275322	0.81[EUR][1000 genomes]
rs61823580	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61823581	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823583	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823585	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823587	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823591	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61824003	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61824005	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61824008	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604724	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604727	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604728	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604729	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604730	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6658954	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6665485	0.85[EUR][1000 genomes]
rs6674541	0.81[EUR][1000 genomes]
rs6674846	0.81[EUR][1000 genomes]
rs6678365	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6682964	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6685557	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6691315	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6694960	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696053	0.82[EUR][1000 genomes]
rs6696222	1.00[ASN][1000 genomes]
rs6700366	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73116425	1.00[ASN][1000 genomes]
rs73116447	1.00[ASN][1000 genomes]
rs73116451	1.00[ASN][1000 genomes]
rs73116456	1.00[ASN][1000 genomes]
rs7331	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7515821	1.00[ASN][1000 genomes]
rs751609	0.81[EUR][1000 genomes]
rs7528455	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7530328	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7535882	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7552702	0.82[EUR][1000 genomes]
rs7555226	0.81[EUR][1000 genomes]
rs898876	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv1008800	chr1:223904653-224061032	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223956600-224004600	Strong transcription	Primary monocytes fromperipheralblood	blood
2	chr1:223956600-224004600	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr1:223960200-223998600	Strong transcription	Fetal Thymus	thymus
4	chr1:223960200-224025400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:223960600-224001400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:223961800-224004400	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr1:223964400-224008000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:223976800-224003000	Weak transcription	Fetal Heart	heart
9	chr1:223979000-224000800	Strong transcription	Primary T helper cells PMA-I stimulated	--
10	chr1:223979200-224002200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:223979400-224002600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:223979600-224002400	Strong transcription	Dnd41	blood
13	chr1:223981800-224002600	Weak transcription	Stomach Mucosa	stomach
14	chr1:223982800-224002200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:223983400-223998000	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr1:223984200-223999400	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr1:223984200-224003000	Strong transcription	K562	blood
18	chr1:223985400-223998000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:223985400-224004000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr1:223988200-224000800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:223988200-224012000	Weak transcription	Colon Smooth Muscle	Colon
22	chr1:223988600-224000600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr1:223990600-224007000	Weak transcription	Fetal Brain Male	brain
24	chr1:223991000-224004400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr1:223991200-223999800	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr1:223991200-223999800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:223991200-223999800	Weak transcription	Brain Germinal Matrix	brain
28	chr1:223991200-223999800	Weak transcription	Brain Hippocampus Middle	brain
29	chr1:223991200-223999800	Weak transcription	Esophagus	oesophagus
30	chr1:223991200-223999800	Weak transcription	NHEK	skin
31	chr1:223991200-224000000	Weak transcription	Gastric	stomach
32	chr1:223991200-224000600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr1:223991200-224000600	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr1:223991200-224000800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr1:223991200-224000800	Weak transcription	Fetal Kidney	kidney
36	chr1:223991200-224000800	Weak transcription	Pancreas	Pancrea
37	chr1:223991200-224007400	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr1:223991200-224007400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr1:223991200-224010800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr1:223991400-223999200	Weak transcription	Brain Substantia Nigra	brain
41	chr1:223991400-223999800	Weak transcription	Right Ventricle	heart
42	chr1:223991400-224007600	Weak transcription	Brain Cingulate Gyrus	brain
43	chr1:223991800-224001200	Weak transcription	Small Intestine	intestine
44	chr1:223992000-223999800	Weak transcription	Thymus	Thymus
45	chr1:223992200-224000600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr1:223992200-224000800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr1:223992400-224000800	Weak transcription	HepG2	liver
48	chr1:223993200-223998600	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr1:223993400-224008400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr1:223993800-223999800	Weak transcription	Aorta	Aorta

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