Variant report

Variant	rs2241714
Chromosome Location	chr19:41869392-41869393
allele	A/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	YY1	chr19:41869344-41871111	A549	lung:	n/a	chr19:41870237-41870259 chr19:41870211-41870221 chr19:41870214-41870222 chr19:41870164-41870180 chr19:41870236-41870248 chr19:41870240-41870248 chr19:41870237-41870247 chr19:41870127-41870136 chr19:41870210-41870222 chr19:41870211-41870221 chr19:41870235-41870254 chr19:41870211-41870233
2	RCOR1	chr19:41869372-41870811	GM12878	blood:	n/a	n/a
3	TEAD4	chr19:41869320-41870795	K562	blood:	n/a	n/a
4	RELA	chr19:41869310-41870686	GM12891	blood:	n/a	chr19:41869689-41869698 chr19:41870397-41870406 chr19:41870397-41870406 chr19:41869689-41869698
5	RELA	chr19:41869257-41870754	GM15510	blood:	n/a	chr19:41869689-41869698 chr19:41870397-41870406 chr19:41870397-41870406 chr19:41869689-41869698
6	POLR2A	chr19:41869301-41871160	SK-N-MC	brain:	n/a	n/a
7	TCF12	chr19:41869359-41870626	A549	lung:	n/a	n/a
8	BHLHE40	chr19:41869223-41870567	GM12878	blood:	n/a	n/a
9	ELF1	chr19:41869214-41870835	A549	lung:	n/a	chr19:41870124-41870136
10	GABPA	chr19:41869381-41870787	A549	lung:	n/a	chr19:41869942-41869951 chr19:41870127-41870136 chr19:41869843-41869854 chr19:41869794-41869803 chr19:41869843-41869852 chr19:41869794-41869805 chr19:41869840-41869854
11	MTA3	chr19:41868956-41871022	GM12878	blood:	n/a	n/a
12	PBX3	chr19:41869191-41871124	A549	lung:	n/a	n/a
13	MAX	chr19:41869392-41870948	A549	lung:	n/a	n/a
14	RELA	chr19:41869321-41870815	GM10847	blood:	n/a	chr19:41869689-41869698 chr19:41870397-41870406 chr19:41870397-41870406 chr19:41869689-41869698
15	MAX	chr19:41869267-41870637	GM12878	blood:	n/a	n/a
16	POLR2A	chr19:41869386-41870584	MCF10A-Er-Src	breast:	n/a	n/a
17	ATF3	chr19:41869231-41870758	A549	lung:	n/a	chr19:41870127-41870136
18	PBX3	chr19:41869338-41870435	A549	lung:	n/a	n/a
19	POLR2A	chr19:41869299-41870743	U87	brain:	n/a	n/a
20	RELA	chr19:41869308-41870697	GM19099	blood:	n/a	chr19:41869689-41869698 chr19:41870397-41870406 chr19:41870397-41870406 chr19:41869689-41869698
21	REST	chr19:41869386-41870803	H1-neurons	neurons:	n/a	chr19:41870346-41870366
22	NRF1	chr19:41869357-41870694	SK-N-SH	brain:	n/a	chr19:41869942-41869951 chr19:41870127-41870136 chr19:41869793-41869804 chr19:41869843-41869854 chr19:41869794-41869803 chr19:41869843-41869852 chr19:41869794-41869805 chr19:41869840-41869854
23	YY1	chr19:41869120-41870675	GM12878	blood:	n/a	chr19:41870237-41870259 chr19:41870211-41870221 chr19:41870214-41870222 chr19:41870164-41870180 chr19:41870236-41870248 chr19:41870240-41870248 chr19:41870237-41870247 chr19:41870127-41870136 chr19:41870210-41870222 chr19:41870211-41870221 chr19:41870235-41870254 chr19:41870211-41870233
24	POLR2A	chr19:41868972-41871020	GM12878	blood:	n/a	n/a
25	HEY1	chr19:41869378-41870531	HepG2	liver:	n/a	n/a
26	BCL3	chr19:41869300-41871014	A549	lung:	n/a	chr19:41870397-41870406 chr19:41870161-41870170
27	POLR2A	chr19:41869166-41870753	GM12878	blood:	n/a	n/a
28	EP300	chr19:41869319-41870672	A549	lung:	n/a	chr19:41870570-41870579 chr19:41870648-41870662 chr19:41869942-41869951
29	POLR2A	chr19:41869029-41870764	HL-60	blood:	n/a	n/a
30	POLR2A	chr19:41869374-41870465	Hela-S3	cervix:	n/a	n/a
31	SIN3AK20	chr19:41869369-41870808	A549	lung:	n/a	n/a
32	MAFK	chr19:41869335-41870755	K562	blood:	n/a	chr19:41870547-41870562
33	POLR2A	chr19:41869293-41870749	U87	brain:	n/a	n/a
34	USF1	chr19:41869372-41870796	A549	lung:	n/a	n/a
35	POLR2A	chr19:41869198-41870812	GM12878	blood:	n/a	n/a
36	WRNIP1	chr19:41869386-41870811	GM12878	blood:	n/a	n/a
37	FOSL2	chr19:41868992-41870941	A549	lung:	n/a	chr19:41870126-41870135 chr19:41869599-41869613
38	POLR2A	chr19:41869183-41870415	K562	blood:	n/a	n/a
39	PAX5	chr19:41869374-41870384	GM12878	blood:	n/a	n/a
40	EP300	chr19:41869336-41870679	GM12878	blood:	n/a	chr19:41870570-41870579 chr19:41870648-41870662 chr19:41869942-41869951
41	POLR2A	chr19:41869323-41870788	GM12892	blood:	n/a	n/a
42	PML	chr19:41869330-41870689	GM12878	blood:	n/a	n/a
43	POLR2A	chr19:41869114-41870958	GM12892	blood:	n/a	n/a
44	POLR2A	chr19:41869379-41871003	K562	blood:	n/a	n/a
45	CHD2	chr19:41869341-41870677	GM12878	blood:	n/a	chr19:41870128-41870138
46	ZNF143	chr19:41869279-41870434	GM12878	blood:	n/a	n/a
47	MXI1	chr19:41869371-41870753	GM12878	blood:	n/a	chr19:41870049-41870064
48	RUNX3	chr19:41869081-41870501	GM12878	blood:	n/a	chr19:41870032-41870049
49	EP300	chr19:41869334-41870752	GM12878	blood:	n/a	chr19:41870570-41870579 chr19:41870648-41870662 chr19:41869942-41869951
50	EBF1	chr19:41869267-41870784	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:41856910..41863042-chr19:41867113..41873191,18	MCF-7	breast:
2	chr19:41868160..41870059-chr19:41902135..41903854,4	K562	blood:
3	chr19:41858489..41863412-chr19:41867730..41871601,11	K562	blood:
4	chr19:41868161..41871707-chr19:41902716..41905358,4	MCF-7	breast:
5	chr19:41868336..41871272-chr19:41944233..41948538,5	K562	blood:
6	chr19:41824554..41827469-chr19:41868894..41871689,2	K562	blood:
7	chr19:41855697..41857432-chr19:41868390..41870729,2	K562	blood:
8	chr19:41868160..41871597-chr19:41899998..41904284,10	K562	blood:
9	chr19:41859483..41864125-chr19:41864354..41869446,7	MCF-7	breast:
10	chr19:41868336..41870018-chr19:41944233..41946275,2	K562	blood:
11	chr19:41814494..41816860-chr19:41868645..41871305,2	K562	blood:
12	chr14:56046261..56047012-chr19:41869306..41870109,2	NB4	blood:

Variant related genes	Relation type
TMEM91	TF binding region
ENSG00000255730	Chromatin interaction
ENSG00000126777	Chromatin interaction
ENSG00000268987	Chromatin interaction
ENSG00000142039	Chromatin interaction
ENSG00000077348	Chromatin interaction
ENSG00000142046	Chromatin interaction
ENSG00000186615	Chromatin interaction
ENSG00000105341	Chromatin interaction
ENSG00000105329	Chromatin interaction
ENSG00000248098	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1025497	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1046909	0.82[JPT][hapmap];0.87[MEX][hapmap]
rs11083616	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11083617	0.99[ASN][1000 genomes]
rs11666933	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs11668109	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11670143	0.98[ASN][1000 genomes]
rs12462166	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12983775	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1549933	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1800469	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1800470	0.93[ASN][1000 genomes]
rs1963413	0.97[ASN][1000 genomes]
rs1982072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2241712	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2241713	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2241715	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2317130	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs284663	0.80[YRI][hapmap]
rs4803457	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs4803458	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4803459	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9797885	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1802868	chr19:41856886-41869392	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
2	nsv521311	chr19:41856886-41882712	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2241714	CEACAM19	cis	cerebellum	SCAN
rs2241714	MGC4093	cis	multi-tissue	Pritchard
rs2241714	GRIN2D	cis	parietal	SCAN
rs2241714	B3GALT7	cis	multi-tissue	Pritchard
rs2241714	LHB	cis	parietal	SCAN
rs2241714	CTC-435M10.6	cis	Whole Blood	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41860400-41869400	Weak transcription	Aorta	Aorta
2	chr19:41860400-41869400	Weak transcription	Ovary	ovary
3	chr19:41868200-41869800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
4	chr19:41868200-41869800	Enhancers	Sigmoid Colon	Sigmoid Colon
5	chr19:41868400-41869400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr19:41868400-41869400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr19:41868600-41869400	Enhancers	Lung	lung
8	chr19:41868600-41869600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
9	chr19:41868800-41869600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
10	chr19:41868800-41869600	Flanking Active TSS	Dnd41	blood
11	chr19:41868800-41869600	Flanking Active TSS	GM12878-XiMat	blood
12	chr19:41869000-41869400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr19:41869000-41869400	Enhancers	Primary B cells from peripheral blood	blood
14	chr19:41869000-41869400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr19:41869000-41869400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
16	chr19:41869000-41869400	Flanking Active TSS	Fetal Brain Female	brain
17	chr19:41869000-41869400	Enhancers	Fetal Muscle Leg	muscle
18	chr19:41869000-41869400	Enhancers	Placenta	Placenta
19	chr19:41869000-41869400	Enhancers	Gastric	stomach
20	chr19:41869000-41869400	Enhancers	Right Atrium	heart
21	chr19:41869000-41869600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr19:41869000-41869600	Flanking Active TSS	Brain Angular Gyrus	brain
23	chr19:41869000-41869600	Flanking Active TSS	Colonic Mucosa	Colon
24	chr19:41869000-41869600	Flanking Active TSS	Duodenum Mucosa	Duodenum
25	chr19:41869000-41869600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
26	chr19:41869000-41869600	Enhancers	Small Intestine	intestine
27	chr19:41869000-41869600	Flanking Active TSS	Stomach Smooth Muscle	stomach
28	chr19:41869000-41869600	Enhancers	Spleen	Spleen
29	chr19:41869000-41869600	Flanking Active TSS	K562	blood
30	chr19:41869000-41869600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
31	chr19:41869000-41869800	Flanking Active TSS	Primary B cells from cord blood	blood
32	chr19:41869000-41869800	Flanking Active TSS	Primary hematopoietic stem cells	blood
33	chr19:41869000-41869800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
34	chr19:41869000-41869800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr19:41869000-41869800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr19:41869000-41869800	Flanking Active TSS	Adipose Nuclei	Adipose
37	chr19:41869000-41870600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr19:41869200-41869400	Enhancers	H1 Cell Line	embryonic stem cell
39	chr19:41869200-41869400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr19:41869200-41869400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr19:41869200-41869400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr19:41869200-41869400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr19:41869200-41869400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr19:41869200-41869400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr19:41869200-41869400	Flanking Active TSS	Brain Germinal Matrix	brain
46	chr19:41869200-41869400	Flanking Active TSS	Brain Hippocampus Middle	brain
47	chr19:41869200-41869400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr19:41869200-41869400	Flanking Active TSS	Brain Substantia Nigra	brain
49	chr19:41869200-41869400	Flanking Active TSS	Esophagus	oesophagus
50	chr19:41869200-41869400	Enhancers	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links