Variant report

Variant	rs420720
Chromosome Location	chr19:41095290-41095291
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:41095150-41095344	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:41095100-41095352	GM12878	blood:	n/a	n/a
3	NFIC	chr19:41095010-41095406	ECC-1	luminal epithelium:	n/a	chr19:41095186-41095203
4	POLR2A	chr19:41094920-41095353	GM12892	blood:	n/a	n/a
5	POLR2A	chr19:41093987-41095369	GM12878	blood:	n/a	n/a
6	POLR2A	chr19:41095124-41095332	H1-hESC	embryonic stem cell:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:41093158..41095920-chr19:41115359..41117293,2	K562	blood:
2	chr19:41089607..41091803-chr19:41093435..41095307,2	MCF-7	breast:
3	chr19:41094390..41097237-chr19:41101497..41103880,2	K562	blood:
4	chr19:41081905..41084190-chr19:41093984..41096140,3	MCF-7	breast:
5	chr19:41081729..41084463-chr19:41093067..41095436,3	MCF-7	breast:
6	chr19:41089392..41091268-chr19:41092459..41096170,3	K562	blood:
7	chr19:41093850..41097927-chr19:41099715..41103880,5	K562	blood:

No data

Variant related genes	Relation type
LTBP4	TF binding region
SHKBP1	TF binding region
ENSG00000090006	Chromatin interaction
ENSG00000160410	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10402698	0.93[ASN][1000 genomes]
rs10403467	0.84[ASN][1000 genomes]
rs10403833	0.85[ASN][1000 genomes]
rs10403963	0.84[ASN][1000 genomes]
rs10405930	0.86[ASN][1000 genomes]
rs10410606	0.86[ASN][1000 genomes]
rs1051303	0.84[ASN][1000 genomes]
rs11083561	0.88[ASN][1000 genomes]
rs1131620	0.83[ASN][1000 genomes]
rs11667706	0.83[ASN][1000 genomes]
rs11667772	0.83[ASN][1000 genomes]
rs12611045	0.84[ASN][1000 genomes]
rs12980111	0.85[ASN][1000 genomes]
rs1318544	0.86[ASN][1000 genomes]
rs1864074	0.87[ASN][1000 genomes]
rs1864078	0.87[ASN][1000 genomes]
rs1869712	0.86[ASN][1000 genomes]
rs2278246	0.84[ASN][1000 genomes]
rs2303727	0.85[ASN][1000 genomes]
rs2303729	0.86[ASN][1000 genomes]
rs2369006	0.85[ASN][1000 genomes]
rs2604902	0.86[ASN][1000 genomes]
rs28649715	0.84[ASN][1000 genomes]
rs28655571	0.85[ASN][1000 genomes]
rs392726	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs393569	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs396118	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs404584	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs406133	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs410101	0.88[ASN][1000 genomes]
rs413901	0.88[ASN][1000 genomes]
rs415075	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs420490	0.84[ASN][1000 genomes]
rs4803348	0.84[ASN][1000 genomes]
rs56353506	0.84[ASN][1000 genomes]
rs7171	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7259067	0.85[ASN][1000 genomes]
rs7259237	0.85[ASN][1000 genomes]
rs7259554	0.85[ASN][1000 genomes]
rs8107014	0.83[ASN][1000 genomes]
rs919307	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	nsv911714	chr19:41006426-41165252	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv911715	chr19:41014922-41141434	Bivalent Enhancer Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers 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	33 gene(s)	inside rSNPs	diseases
4	nsv1057634	chr19:41019512-41174259	Enhancers Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv911716	chr19:41023511-41109456	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv911717	chr19:41023511-41141434	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv911719	chr19:41033109-41147087	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
8	nsv911720	chr19:41033109-41156940	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
9	nsv911721	chr19:41040334-41124931	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
10	nsv911722	chr19:41040334-41176403	Bivalent Enhancer Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
11	nsv911723	chr19:41075990-41195279	Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
12	nsv869561	chr19:41077513-41139834	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
13	nsv1064699	chr19:41086506-41174259	Genic enhancers Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
14	nsv911724	chr19:41089505-41165252	Bivalent/Poised TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
15	nsv911725	chr19:41090190-41114065	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
16	nsv911726	chr19:41090190-41141434	Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs420720	SHKBP1	Cis_1M	lymphoblastoid	RTeQTL
rs420720	SHKBP1	cis	Whole Blood	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41083600-41095400	Weak transcription	Fetal Kidney	kidney
2	chr19:41083600-41100400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr19:41083600-41101000	Weak transcription	HSMMtube	muscle
4	chr19:41084000-41095400	Strong transcription	Fetal Intestine Small	intestine
5	chr19:41084000-41097600	Strong transcription	Fetal Stomach	stomach
6	chr19:41084200-41099800	Weak transcription	Fetal Brain Male	brain
7	chr19:41084400-41100000	Weak transcription	Stomach Mucosa	stomach
8	chr19:41084600-41097600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr19:41084600-41100400	Weak transcription	NHDF-Ad	bronchial
10	chr19:41084600-41102600	Weak transcription	Right Atrium	heart
11	chr19:41084800-41096600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr19:41084800-41097200	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr19:41084800-41097600	Strong transcription	Thymus	Thymus
14	chr19:41085400-41097200	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr19:41086000-41097200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr19:41086000-41097800	Strong transcription	Primary T cells from cord blood	blood
17	chr19:41086400-41100400	Weak transcription	K562	blood
18	chr19:41086600-41097400	Strong transcription	Primary B cells from peripheral blood	blood
19	chr19:41086800-41097400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr19:41086800-41097400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr19:41086800-41099000	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr19:41086800-41100000	Weak transcription	Fetal Brain Female	brain
23	chr19:41086800-41100600	Weak transcription	Brain Angular Gyrus	brain
24	chr19:41087000-41097000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr19:41087000-41097200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr19:41087200-41096800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr19:41087200-41100400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr19:41087600-41102600	Weak transcription	Small Intestine	intestine
29	chr19:41087800-41095600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr19:41087800-41098200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr19:41087800-41100000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr19:41088400-41095800	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr19:41088400-41100200	Weak transcription	Brain Substantia Nigra	brain
34	chr19:41088600-41100200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr19:41089200-41100400	Weak transcription	Brain Cingulate Gyrus	brain
36	chr19:41089400-41098200	Weak transcription	Brain Germinal Matrix	brain
37	chr19:41089600-41095800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr19:41090400-41096800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr19:41090600-41099600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr19:41090800-41100000	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr19:41091400-41097200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr19:41091400-41100000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr19:41091600-41095600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr19:41092400-41095400	Weak transcription	GM12878-XiMat	blood
45	chr19:41092400-41097000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr19:41092400-41097000	Strong transcription	Esophagus	oesophagus
47	chr19:41092400-41097000	Strong transcription	NHLF	lung
48	chr19:41092400-41097400	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr19:41092600-41095600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr19:41092600-41096200	Strong transcription	Colonic Mucosa	Colon

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