Variant report

Variant	rs406133
Chromosome Location	chr19:41091821-41091822
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr19:41091637-41091956	MCF10A-Er-Src	breast:	n/a	n/a
2	EP300	chr19:41091272-41092232	A549	lung:	n/a	chr19:41092082-41092096 chr19:41092076-41092090
3	POLR2A	chr19:41091439-41091954	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr19:41091340-41092119	U87	brain:	n/a	n/a
5	TCF7L2	chr19:41091635-41091968	Hela-S3	cervix:	n/a	n/a
6	ELK4	chr19:41091490-41092021	Hela-S3	cervix:	n/a	n/a
7	CEBPB	chr19:41091694-41091990	K562	blood:	n/a	chr19:41091867-41091878
8	MAX	chr19:41091703-41091943	NB4	blood:	n/a	n/a
9	YY1	chr19:41091593-41091983	A549	lung:	n/a	n/a
10	POLR2A	chr19:41091464-41092029	HUVEC	blood vessel:	n/a	n/a
11	RFX5	chr19:41091725-41091918	Hela-S3	cervix:	n/a	n/a
12	MAX	chr19:41090927-41092350	A549	lung:	n/a	n/a
13	SIX5	chr19:41090616-41092588	A549	lung:	n/a	n/a
14	STAT3	chr19:41091576-41092012	Hela-S3	cervix:	n/a	n/a
15	FOS	chr19:41091606-41092029	MCF10A-Er-Src	breast:	n/a	chr19:41091762-41091773
16	SP1	chr19:41091229-41092156	A549	lung:	n/a	n/a
17	RCOR1	chr19:41091629-41092028	Hela-S3	cervix:	n/a	n/a
18	CEBPB	chr19:41091355-41092073	A549	lung:	n/a	chr19:41091867-41091878
19	CEBPB	chr19:41091458-41092035	IMR90	lung:	n/a	chr19:41091867-41091878
20	EP300	chr19:41091596-41092000	Hela-S3	cervix:	n/a	n/a
21	FOS	chr19:41091654-41092008	MCF10A-Er-Src	breast:	n/a	chr19:41091762-41091773
22	GATA3	chr19:41091376-41092274	A549	lung:	n/a	n/a
23	SMC3	chr19:41091715-41092004	Hela-S3	cervix:	n/a	n/a
24	FOS	chr19:41091553-41092030	MCF10A-Er-Src	breast:	n/a	chr19:41091762-41091773
25	CREB1	chr19:41091660-41092066	A549	lung:	n/a	n/a
26	USF1	chr19:41091588-41091930	A549	lung:	n/a	n/a
27	MYC	chr19:41091730-41091948	NB4	blood:	n/a	n/a
28	EP300	chr19:41091458-41092300	A549	lung:	n/a	chr19:41092082-41092096 chr19:41092076-41092090
29	SIN3AK20	chr19:41091650-41091940	PFSK-1	brain:	n/a	n/a
30	POLR2A	chr19:41091531-41091917	Hela-S3	cervix:	n/a	n/a
31	USF2	chr19:41091576-41091930	Hela-S3	cervix:	n/a	n/a
32	MAX	chr19:41091617-41092156	A549	lung:	n/a	n/a
33	MYC	chr19:41091606-41092030	MCF10A-Er-Src	breast:	n/a	n/a
34	STAT3	chr19:41091295-41091997	MCF10A-Er-Src	breast:	n/a	n/a
35	BCL3	chr19:41091545-41092086	A549	lung:	n/a	n/a
36	GABPA	chr19:41091541-41092057	A549	lung:	n/a	n/a
37	ATF3	chr19:41091541-41092082	A549	lung:	n/a	n/a
38	ZBTB33	chr19:41091635-41092031	A549	lung:	n/a	n/a
39	E2F6	chr19:41091412-41092343	A549	lung:	n/a	n/a
40	MAX	chr19:41091625-41092032	Hela-S3	cervix:	n/a	n/a
41	STAT3	chr19:41091718-41091923	MCF10A-Er-Src	breast:	n/a	n/a
42	REST	chr19:41091628-41091934	PFSK-1	brain:	n/a	n/a
43	CEBPB	chr19:41091318-41092089	Hela-S3	cervix:	n/a	chr19:41091867-41091878
44	CEBPB	chr19:41091638-41091997	MCF-7	breast:	n/a	chr19:41091867-41091878
45	TAF1	chr19:41091557-41091859	Hela-S3	cervix:	n/a	n/a
46	USF1	chr19:41091452-41092280	A549	lung:	n/a	n/a
47	CEBPB	chr19:41091188-41092349	A549	lung:	n/a	chr19:41091867-41091878
48	FOXA2	chr19:41091517-41092158	A549	lung:	n/a	n/a
49	MYC	chr19:41091719-41091866	Hela-S3	cervix:	n/a	n/a
50	CEBPB	chr19:41091229-41092176	A549	lung:	n/a	chr19:41091867-41091878

No.	Distal block	Cell Line	Cell type
1	chr19:41082792..41084497-chr19:41089629..41092124,2	MCF-7	breast:
2	chr19:41083433..41086530-chr19:41091695..41093965,3	MCF-7	breast:
3	chr19:41089494..41092756-chr19:41107049..41110047,4	K562	blood:

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

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10402698	0.95[ASN][1000 genomes]
rs10403467	0.82[ASN][1000 genomes]
rs10403833	0.82[ASN][1000 genomes]
rs10403963	0.82[ASN][1000 genomes]
rs10405930	0.83[ASN][1000 genomes]
rs10410606	0.83[ASN][1000 genomes]
rs1051303	0.80[ASN][1000 genomes]
rs11083561	0.85[ASN][1000 genomes]
rs11667706	0.81[ASN][1000 genomes]
rs11667772	0.81[ASN][1000 genomes]
rs12611045	0.80[ASN][1000 genomes]
rs12980111	0.82[ASN][1000 genomes]
rs1318544	0.83[ASN][1000 genomes]
rs1864074	0.85[ASN][1000 genomes]
rs1864078	0.85[ASN][1000 genomes]
rs1869712	0.83[ASN][1000 genomes]
rs2278246	0.80[ASN][1000 genomes]
rs2303727	0.82[ASN][1000 genomes]
rs2303729	0.83[ASN][1000 genomes]
rs2369006	0.81[ASN][1000 genomes]
rs2604902	0.83[ASN][1000 genomes]
rs28649715	0.82[ASN][1000 genomes]
rs28655571	0.82[ASN][1000 genomes]
rs392726	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs393569	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs396118	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs404584	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs410101	0.90[ASN][1000 genomes]
rs413901	0.90[ASN][1000 genomes]
rs415075	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs420490	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs420720	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4803348	0.80[ASN][1000 genomes]
rs56353506	0.82[ASN][1000 genomes]
rs7171	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7259067	0.82[ASN][1000 genomes]
rs7259237	0.82[ASN][1000 genomes]
rs7259554	0.82[ASN][1000 genomes]
rs8107014	0.81[ASN][1000 genomes]
rs919307	0.83[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs406133	SHKBP1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41083600-41092800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:41083600-41093600	Weak transcription	Fetal Lung	lung
3	chr19:41083600-41095400	Weak transcription	Fetal Kidney	kidney
4	chr19:41083600-41100400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr19:41083600-41101000	Weak transcription	HSMMtube	muscle
6	chr19:41084000-41094000	Weak transcription	HSMM	muscle
7	chr19:41084000-41095400	Strong transcription	Fetal Intestine Small	intestine
8	chr19:41084000-41097600	Strong transcription	Fetal Stomach	stomach
9	chr19:41084200-41093800	Weak transcription	NHEK	skin
10	chr19:41084200-41099800	Weak transcription	Fetal Brain Male	brain
11	chr19:41084400-41092000	Weak transcription	HepG2	liver
12	chr19:41084400-41094200	Weak transcription	HMEC	breast
13	chr19:41084400-41100000	Weak transcription	Stomach Mucosa	stomach
14	chr19:41084600-41095200	Strong transcription	Fetal Muscle Leg	muscle
15	chr19:41084600-41097600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr19:41084600-41100400	Weak transcription	NHDF-Ad	bronchial
17	chr19:41084600-41102600	Weak transcription	Right Atrium	heart
18	chr19:41084800-41096600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr19:41084800-41097200	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr19:41084800-41097600	Strong transcription	Thymus	Thymus
21	chr19:41085200-41094000	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr19:41085400-41094800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr19:41085400-41097200	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr19:41085800-41095200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr19:41085800-41095200	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr19:41086000-41094600	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr19:41086000-41094800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr19:41086000-41095200	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr19:41086000-41095200	Strong transcription	Stomach Smooth Muscle	stomach
30	chr19:41086000-41097200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr19:41086000-41097800	Strong transcription	Primary T cells from cord blood	blood
32	chr19:41086400-41100400	Weak transcription	K562	blood
33	chr19:41086600-41097400	Strong transcription	Primary B cells from peripheral blood	blood
34	chr19:41086800-41097400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr19:41086800-41097400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr19:41086800-41099000	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr19:41086800-41100000	Weak transcription	Fetal Brain Female	brain
38	chr19:41086800-41100600	Weak transcription	Brain Angular Gyrus	brain
39	chr19:41087000-41092800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr19:41087000-41093400	Strong transcription	Primary hematopoietic stem cells	blood
41	chr19:41087000-41097000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr19:41087000-41097200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr19:41087200-41096800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr19:41087200-41100400	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr19:41087600-41102600	Weak transcription	Small Intestine	intestine
46	chr19:41087800-41093200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr19:41087800-41095600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr19:41087800-41098200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr19:41087800-41100000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr19:41088400-41092600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links