Variant report

Variant	rs11673492
Chromosome Location	chr19:41220529-41220530
allele	C/T
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	MAX	chr19:41220113-41225416	A549	lung:	n/a	chr19:41225122-41225132 chr19:41222713-41222723 chr19:41222082-41222091
2	SP1	chr19:41220495-41223600	A549	lung:	n/a	chr19:41222709-41222723 chr19:41220745-41220759 chr19:41222798-41222807 chr19:41222861-41222870 chr19:41221025-41221034 chr19:41222705-41222716 chr19:41222861-41222870 chr19:41222860-41222870 chr19:41221456-41221470 chr19:41222599-41222611 chr19:41222860-41222869 chr19:41222859-41222871 chr19:41221602-41221611 chr19:41222599-41222611 chr19:41222796-41222808 chr19:41221879-41221893 chr19:41222859-41222871 chr19:41222919-41222928 chr19:41221600-41221612 chr19:41222969-41222979 chr19:41222600-41222609 chr19:41222969-41222979
3	SIN3AK20	chr19:41220394-41220909	A549	lung:	n/a	n/a
4	BCL3	chr19:41220248-41225401	A549	lung:	n/a	chr19:41225228-41225237 chr19:41222875-41222884 chr19:41222082-41222091 chr19:41222234-41222243
5	TCF12	chr19:41220427-41223301	SK-N-SH	brain:	n/a	chr19:41221137-41221145
6	POLR2A	chr19:41220316-41225389	H1-hESC	embryonic stem cell:	n/a	n/a
7	ELF1	chr19:41220446-41221891	A549	lung:	n/a	chr19:41221003-41221016 chr19:41221005-41221014
8	REST	chr19:41220437-41223042	A549	lung:	n/a	chr19:41222176-41222196 chr19:41221597-41221607
9	POLR2A	chr19:41220210-41223292	SK-N-MC	brain:	n/a	n/a
10	ELF1	chr19:41220488-41223034	A549	lung:	n/a	chr19:41221003-41221016 chr19:41221005-41221014
11	POLR2A	chr19:41220314-41228780	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr19:41220367-41223130	SK-N-SH	brain:	n/a	n/a
13	SIN3AK20	chr19:41220499-41225010	A549	lung:	n/a	n/a
14	POLR2A	chr19:41220376-41228744	MCF10A-Er-Src	breast:	n/a	n/a
15	RELA	chr19:41220457-41223865	GM12891	blood:	n/a	chr19:41222874-41222883 chr19:41222874-41222883
16	MXI1	chr19:41220156-41225428	IMR90	lung:	n/a	n/a
17	MAX	chr19:41220045-41225483	A549	lung:	n/a	chr19:41225122-41225132 chr19:41222713-41222723 chr19:41222082-41222091
18	POLR2A	chr19:41220362-41221292	A549	lung:	n/a	n/a
19	ELF1	chr19:41219985-41220569	GM12878	blood:	n/a	n/a
20	CREB1	chr19:41220384-41221306	A549	lung:	n/a	n/a
21	POLR2A	chr19:41220506-41224248	K562	blood:	n/a	n/a
22	STAT3	chr19:41220517-41223080	MCF10A-Er-Src	breast:	n/a	chr19:41222081-41222090 chr19:41221661-41221669 chr19:41222150-41222162 chr19:41221879-41221891 chr19:41220853-41220865 chr19:41221659-41221670
23	ATF3	chr19:41220456-41223157	A549	lung:	n/a	chr19:41221025-41221034 chr19:41222918-41222927 chr19:41222622-41222631
24	SP1	chr19:41220260-41223826	A549	lung:	n/a	chr19:41222709-41222723 chr19:41220745-41220759 chr19:41222798-41222807 chr19:41222861-41222870 chr19:41221025-41221034 chr19:41222705-41222716 chr19:41222861-41222870 chr19:41222860-41222870 chr19:41221456-41221470 chr19:41222599-41222611 chr19:41222860-41222869 chr19:41222859-41222871 chr19:41221602-41221611 chr19:41222599-41222611 chr19:41222796-41222808 chr19:41221879-41221893 chr19:41222859-41222871 chr19:41222919-41222928 chr19:41221600-41221612 chr19:41222969-41222979 chr19:41222600-41222609 chr19:41222969-41222979
25	MTA3	chr19:41220307-41223151	GM12878	blood:	n/a	n/a
26	REST	chr19:41220420-41223043	A549	lung:	n/a	chr19:41222176-41222196 chr19:41221597-41221607
27	GABPA	chr19:41220478-41223176	A549	lung:	n/a	chr19:41221602-41221611
28	POLR2A	chr19:41220494-41223478	GM19099	blood:	n/a	n/a
29	POLR2A	chr19:41220464-41221301	SK-N-SH	brain:	n/a	n/a
30	TCF12	chr19:41220164-41225474	A549	lung:	n/a	chr19:41221137-41221145
31	POLR2A	chr19:41220409-41223578	U87	brain:	n/a	n/a
32	STAT1	chr19:41220400-41224080	Hela-S3	cervix:	n/a	chr19:41222081-41222090 chr19:41221659-41221670 chr19:41221661-41221669 chr19:41222150-41222162 chr19:41221879-41221891 chr19:41220853-41220865
33	EBF1	chr19:41220340-41223034	GM12878	blood:	n/a	n/a
34	PBX3	chr19:41220195-41223188	A549	lung:	n/a	n/a
35	POLR2A	chr19:41220360-41220618	A549	lung:	n/a	n/a
36	REST	chr19:41220341-41223836	H1-neurons	neurons:	n/a	chr19:41222176-41222196 chr19:41221597-41221607
37	FOSL2	chr19:41220277-41224942	A549	lung:	n/a	chr19:41221814-41221824 chr19:41222178-41222189 chr19:41222081-41222091 chr19:41221813-41221825 chr19:41222081-41222091 chr19:41222917-41222926 chr19:41222081-41222091 chr19:41221815-41221823 chr19:41222179-41222189 chr19:41222081-41222091 chr19:41222081-41222090
38	GATA3	chr19:41220515-41224110	A549	lung:	n/a	chr19:41222790-41222798
39	POLR2A	chr19:41220415-41223171	U87	brain:	n/a	n/a
40	EP300	chr19:41220428-41223201	A549	lung:	n/a	chr19:41222082-41222091
41	MAZ	chr19:41220232-41225451	IMR90	lung:	n/a	chr19:41222713-41222723 chr19:41222082-41222091
42	SIX5	chr19:41220157-41223969	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:41219466..41223288-chr19:41281896..41285456,5	MCF-7	breast:
2	chr19:41220369..41226479-chr19:41305318..41310706,7	K562	blood:
3	chr19:41220005..41225073-chr19:41230462..41235365,8	K562	blood:
4	chr19:41220377..41222544-chr19:41768201..41769798,2	MCF-7	breast:
5	chr19:41213611..41215968-chr19:41219093..41222083,3	MCF-7	breast:
6	chr19:41219701..41226727-chr19:41253156..41258804,17	K562	blood:
7	chr19:41219692..41221966-chr19:41769353..41771568,2	MCF-7	breast:
8	chr19:41188510..41190194-chr19:41220428..41221993,2	K562	blood:
9	chr19:41191453..41200740-chr19:41219595..41226457,20	MCF-7	breast:
10	chr19:40949565..40951989-chr19:41219354..41222014,2	K562	blood:
11	chr19:41220057..41225402-chr19:41302090..41307926,9	MCF-7	breast:
12	chr19:41195568..41198287-chr19:41219071..41220657,2	K562	blood:
13	chr19:41220238..41223312-chr19:41303618..41307521,4	K562	blood:
14	chr19:41219701..41225554-chr19:41255271..41259667,13	K562	blood:
15	chr19:40948713..40950768-chr19:41219384..41222098,2	K562	blood:
16	chr19:41219625..41226874-chr19:41252287..41258959,29	MCF-7	breast:
17	chr19:41193720..41198590-chr19:41218677..41224410,19	MCF-7	breast:
18	chr19:41219350..41226574-chr19:41253922..41258567,22	MCF-7	breast:

Variant related genes	Relation type
ITPKC	TF binding region
ENSG00000268366	Chromatin interaction
ENSG00000188493	Chromatin interaction
ENSG00000261857	Chromatin interaction
ENSG00000268797	Chromatin interaction
ENSG00000086544	Chromatin interaction
ENSG00000077312	Chromatin interaction
ENSG00000105323	Chromatin interaction
ENSG00000105245	Chromatin interaction
ENSG00000269858	Chromatin interaction
ENSG00000167578	Chromatin interaction
ENSG00000171570	Chromatin interaction
ENSG00000223284	Chromatin interaction
ENSG00000167565	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11665867	0.87[ASW][hapmap]
rs11668501	1.00[ASW][hapmap];0.94[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11671127	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12975396	0.89[ASW][hapmap];1.00[CHB][hapmap]
rs12983335	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12984298	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12984927	1.00[CHB][hapmap]
rs4420642	0.94[EUR][1000 genomes]
rs67083521	0.91[EUR][1000 genomes]
rs7253502	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7253804	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8105009	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	esv1800615	chr19:41127465-41270055	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv1067017	chr19:41185992-41231251	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11673492	STRN4	cis	parietal	SCAN
rs11673492	APOC4	cis	cerebellum	SCAN
rs11673492	EMP3	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41197200-41220600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr19:41208800-41221000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr19:41212200-41220600	Weak transcription	Aorta	Aorta
4	chr19:41219000-41220800	Enhancers	Spleen	Spleen
5	chr19:41219800-41220800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr19:41219800-41221000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr19:41219800-41222600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr19:41219800-41222800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr19:41220000-41220600	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr19:41220000-41220800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
11	chr19:41220000-41220800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr19:41220000-41220800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr19:41220000-41220800	Flanking Active TSS	A549	lung
14	chr19:41220000-41222600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr19:41220200-41220600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr19:41220200-41220600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:41220200-41220600	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr19:41220200-41220600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr19:41220200-41220600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr19:41220200-41220600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
21	chr19:41220200-41220600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr19:41220200-41220600	Flanking Active TSS	Brain Anterior Caudate	brain
23	chr19:41220200-41220600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr19:41220200-41220600	Flanking Active TSS	Brain Substantia Nigra	brain
25	chr19:41220200-41220600	Flanking Active TSS	Right Atrium	heart
26	chr19:41220200-41220600	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr19:41220200-41220600	Flanking Active TSS	Stomach Smooth Muscle	stomach
28	chr19:41220200-41220600	Flanking Active TSS	GM12878-XiMat	blood
29	chr19:41220200-41220600	Flanking Active TSS	HepG2	liver
30	chr19:41220200-41220600	Flanking Active TSS	NHEK	skin
31	chr19:41220200-41220600	Flanking Active TSS	NHLF	lung
32	chr19:41220200-41220800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr19:41220200-41220800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
34	chr19:41220200-41220800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
35	chr19:41220200-41220800	Flanking Active TSS	Primary T cells from cord blood	blood
36	chr19:41220200-41220800	Flanking Active TSS	Primary hematopoietic stem cells	blood
37	chr19:41220200-41220800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
38	chr19:41220200-41220800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr19:41220200-41220800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
40	chr19:41220200-41220800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr19:41220200-41220800	Flanking Active TSS	Brain Cingulate Gyrus	brain
42	chr19:41220200-41220800	Flanking Active TSS	Brain Germinal Matrix	brain
43	chr19:41220200-41220800	Flanking Active TSS	Brain Hippocampus Middle	brain
44	chr19:41220200-41220800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
45	chr19:41220200-41220800	Flanking Active TSS	Colonic Mucosa	Colon
46	chr19:41220200-41220800	Flanking Active TSS	Colon Smooth Muscle	Colon
47	chr19:41220200-41220800	Flanking Active TSS	Fetal Brain Female	brain
48	chr19:41220200-41220800	Flanking Active TSS	Fetal Thymus	thymus
49	chr19:41220200-41220800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
50	chr19:41220200-41220800	Flanking Active TSS	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links