Variant report

Variant	rs56041141
Chromosome Location	chr4:15599845-15599846
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:15599091..15600880-chr4:15606438..15609058,2	K562	blood:

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10003739	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10008875	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10008889	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10012838	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10017295	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10020408	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10022610	0.85[AFR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10025837	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10026851	0.90[AFR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10030313	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10031017	0.90[AFR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10034328	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10939621	0.82[ASN][1000 genomes]
rs10939628	0.97[AFR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1134634	0.92[ASN][1000 genomes]
rs11932730	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11933521	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11939541	0.90[AFR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11942335	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11943107	0.95[AFR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11945626	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12503015	0.88[EUR][1000 genomes]
rs12508186	0.85[EUR][1000 genomes]
rs12509029	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12511894	0.85[EUR][1000 genomes]
rs12640192	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12644327	0.90[AFR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12645849	0.90[AFR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12649803	0.83[ASN][1000 genomes]
rs13104845	0.81[ASN][1000 genomes]
rs13116304	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13121363	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1473166	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16892140	0.81[AFR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16892152	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2041671	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2110361	0.82[ASN][1000 genomes]
rs2160044	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28419165	0.97[AFR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28522268	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28528670	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28534607	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28661857	0.97[AFR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3822298	0.83[AFR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4235380	0.88[AFR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4279203	0.83[EUR][1000 genomes]
rs4280723	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4280724	0.92[AFR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4393989	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4583752	0.88[AFR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4591601	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4642244	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4698117	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4698403	0.90[AFR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4698405	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4698408	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57526178	0.91[AFR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59055524	0.82[ASN][1000 genomes]
rs60813847	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62290565	0.83[ASN][1000 genomes]
rs62290605	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6449146	0.83[ASN][1000 genomes]
rs6449147	0.83[ASN][1000 genomes]
rs6449149	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6831286	0.84[AFR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6839438	0.97[AFR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73125606	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73125616	0.85[EUR][1000 genomes]
rs73125627	0.87[EUR][1000 genomes]
rs73125637	0.87[EUR][1000 genomes]
rs73127647	0.90[AFR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7377825	0.91[AFR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs741180	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs759212	0.83[ASN][1000 genomes]
rs7661102	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7665390	0.92[AFR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7665915	0.90[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7682586	0.90[AFR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7687010	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7697314	0.81[ASN][1000 genomes]
rs872678	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9996452	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv428439	chr4:15556961-15749520	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1012988	chr4:15597510-16091527	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15537400-15621000	Weak transcription	Hela-S3	cervix
2	chr4:15550000-15617800	Weak transcription	Thymus	Thymus
3	chr4:15554600-15601400	Weak transcription	A549	lung
4	chr4:15556000-15603200	Weak transcription	Fetal Thymus	thymus
5	chr4:15564000-15600600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr4:15564400-15603200	Weak transcription	HMEC	breast
7	chr4:15564600-15603600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr4:15565400-15612600	Weak transcription	Brain Substantia Nigra	brain
9	chr4:15565400-15621400	Weak transcription	Esophagus	oesophagus
10	chr4:15565600-15604200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr4:15565600-15611400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr4:15565800-15605000	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr4:15568400-15655600	Weak transcription	Gastric	stomach
14	chr4:15569600-15603600	Weak transcription	Spleen	Spleen
15	chr4:15569600-15604200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr4:15570200-15601800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr4:15570600-15602000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr4:15570600-15602000	Weak transcription	Pancreas	Pancrea
19	chr4:15572200-15601200	Weak transcription	NHLF	lung
20	chr4:15572200-15601800	Weak transcription	Brain Angular Gyrus	brain
21	chr4:15572200-15601800	Weak transcription	NHEK	skin
22	chr4:15572200-15604000	Weak transcription	Primary T cells from cord blood	blood
23	chr4:15572200-15604200	Weak transcription	Duodenum Mucosa	Duodenum
24	chr4:15573200-15603800	Weak transcription	Fetal Intestine Small	intestine
25	chr4:15575200-15618000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr4:15577800-15602800	Weak transcription	Placenta	Placenta
27	chr4:15580400-15600000	Weak transcription	Colon Smooth Muscle	Colon
28	chr4:15587200-15612600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr4:15588200-15601200	Weak transcription	Primary B cells from cord blood	blood
30	chr4:15589000-15600000	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr4:15589200-15602800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr4:15589600-15602000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr4:15589600-15603000	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr4:15589800-15621400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr4:15590000-15603200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr4:15590000-15615600	Weak transcription	Lung	lung
37	chr4:15590400-15604200	Weak transcription	Fetal Intestine Large	intestine
38	chr4:15590600-15626400	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr4:15593800-15604200	Weak transcription	Brain Germinal Matrix	brain
40	chr4:15593800-15621200	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr4:15594000-15601400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr4:15594000-15601600	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr4:15594000-15603600	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr4:15594000-15607200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr4:15594000-15609200	Weak transcription	Psoas Muscle	Psoas
46	chr4:15594200-15601600	Weak transcription	Fetal Brain Female	brain
47	chr4:15594200-15604400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr4:15594600-15617800	Weak transcription	Right Ventricle	heart
49	chr4:15595000-15604400	Weak transcription	HUVEC	blood vessel
50	chr4:15595000-15604600	Weak transcription	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links