Variant report

Variant	rs6057242
Chromosome Location	chr20:29519757-29519758
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11152497	0.92[ASN][1000 genomes]
rs12624703	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13042647	0.93[ASN][1000 genomes]
rs13042691	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1811868	0.86[ASN][1000 genomes]
rs1969705	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1969706	0.94[ASN][1000 genomes]
rs1969708	0.86[ASN][1000 genomes]
rs2424800	0.89[ASN][1000 genomes]
rs2424804	0.84[ASN][1000 genomes]
rs2424806	0.83[ASN][1000 genomes]
rs35034389	0.88[ASN][1000 genomes]
rs4010752	0.93[ASN][1000 genomes]
rs57163531	1.00[ASN][1000 genomes]
rs6057136	0.94[ASN][1000 genomes]
rs6057239	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6057243	0.94[ASN][1000 genomes]
rs6057254	0.83[AFR][1000 genomes]
rs6057528	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6057529	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6087199	0.94[ASN][1000 genomes]
rs6087200	0.94[ASN][1000 genomes]
rs6087205	0.86[ASN][1000 genomes]
rs6118964	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6118965	0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6118967	0.89[ASN][1000 genomes]
rs6118970	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6118971	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6118975	0.94[ASN][1000 genomes]
rs6118976	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6118977	0.94[ASN][1000 genomes]
rs6118978	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6119216	0.87[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6119220	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6567440	0.86[ASN][1000 genomes]
rs6567482	0.92[ASN][1000 genomes]
rs7272651	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73608593	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8113960	0.85[ASN][1000 genomes]
rs8122227	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758518	chr20:29419570-29653908	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	esv2758791	chr20:29419570-29653908	ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv428028	chr20:29419570-29653908	Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv428376	chr20:29419570-29653908	Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1056924	chr20:29420340-29529915	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1061714	chr20:29420340-29560603	Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1059061	chr20:29420340-29598851	Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1062766	chr20:29420340-29635454	ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	esv2763660	chr20:29420352-29552211	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv585866	chr20:29425357-29558463	Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv964388	chr20:29425430-29521699	ZNF genes & repeats Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv585867	chr20:29429945-29522520	Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	esv2756708	chr20:29444244-29609067	ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv1062061	chr20:29448943-29560603	Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	nsv833950	chr20:29472154-29638425	Weak transcription ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
16	nsv1058387	chr20:29479828-29651199	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
17	esv2756736	chr20:29493193-29630695	ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
18	esv1002752	chr20:29505919-29570446	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
19	nsv436324	chr20:29508007-29536744	Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
20	nsv512608	chr20:29508738-29536138	Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
21	esv3515439	chr20:29508921-29536159	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
22	esv3515440	chr20:29508938-29536132	Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
23	esv3515442	chr20:29509063-29536054	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
24	nsv9803	chr20:29510801-29535963	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
25	nsv979453	chr20:29511046-29521699	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
26	esv3420534	chr20:29516391-29520589	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6057242	RP4-610C12.4	cis	lung	GTEx

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:29517800-29519800	ZNF genes & repeats	Brain Germinal Matrix	brain
2	chr20:29518200-29519800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr20:29518200-29519800	ZNF genes & repeats	Fetal Stomach	stomach
4	chr20:29518200-29520000	Active TSS	Brain Angular Gyrus	brain
5	chr20:29518200-29520000	Active TSS	Fetal Kidney	kidney
6	chr20:29518400-29519800	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr20:29518600-29521200	Transcr. at gene 5' and 3'	Dnd41	blood
8	chr20:29519000-29519800	Enhancers	Primary T cells fromperipheralblood	blood
9	chr20:29519000-29520000	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr20:29519000-29520200	Active TSS	Brain Cingulate Gyrus	brain
11	chr20:29519000-29521200	Active TSS	Brain Anterior Caudate	brain
12	chr20:29519000-29523800	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr20:29519000-29524200	Weak transcription	Small Intestine	intestine
14	chr20:29519000-29524400	Weak transcription	Primary T cells from cord blood	blood
15	chr20:29519000-29524400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr20:29519000-29524400	Weak transcription	Aorta	Aorta
17	chr20:29519000-29524800	Weak transcription	Primary B cells from cord blood	blood
18	chr20:29519200-29520000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr20:29519200-29523000	Weak transcription	Right Atrium	heart
20	chr20:29519200-29523600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr20:29519200-29523800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr20:29519200-29523800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr20:29519200-29523800	Weak transcription	Osteobl	bone
24	chr20:29519200-29524200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr20:29519200-29524200	Weak transcription	HSMMtube	muscle
26	chr20:29519400-29521000	Weak transcription	Primary B cells from peripheral blood	blood
27	chr20:29519400-29523800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr20:29519400-29523800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr20:29519400-29524200	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr20:29519400-29525000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr20:29519600-29519800	Enhancers	Stomach Mucosa	stomach
32	chr20:29519600-29519800	Bivalent Enhancer	Stomach Smooth Muscle	stomach
33	chr20:29519600-29520200	Active TSS	Pancreas	Pancrea
34	chr20:29519600-29520400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr20:29519600-29520400	Weak transcription	Esophagus	oesophagus
36	chr20:29519600-29520400	Weak transcription	K562	blood
37	chr20:29519600-29520600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr20:29519600-29520600	Weak transcription	Duodenum Mucosa	Duodenum
39	chr20:29519600-29520600	Weak transcription	Gastric	stomach
40	chr20:29519600-29520800	Weak transcription	Spleen	Spleen
41	chr20:29519600-29522200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr20:29519600-29522800	Weak transcription	Primary hematopoietic stem cells	blood
43	chr20:29519600-29523000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr20:29519600-29523200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr20:29519600-29523200	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr20:29519600-29523600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr20:29519600-29523600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr20:29519600-29523600	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr20:29519600-29523600	Weak transcription	Thymus	Thymus
50	chr20:29519600-29523600	Weak transcription	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links