Variant report

Variant	rs11880261
Chromosome Location	chr19:40788641-40788642
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	POLR2A	chr19:40788195-40792187	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr19:40788136-40791242	GM12878	blood:	n/a	n/a
3	POLR2A	chr19:40781762-40793937	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr19:40787276-40792053	GM12878	blood:	n/a	n/a
5	SIN3AK20	chr19:40787407-40793117	PANC-1	pancreas:	n/a	n/a
6	REST	chr19:40787574-40792112	PANC-1	pancreas:	n/a	chr19:40790862-40790875 chr19:40789693-40789706 chr19:40790806-40790816 chr19:40789758-40789768

No.	Distal block	Cell Line	Cell type
1	chr19:40695407..40698481-chr19:40788292..40792778,5	K562	blood:
2	chr19:40731324..40733318-chr19:40786434..40789035,2	MCF-7	breast:
3	chr19:40787579..40789839-chr19:40846986..40849835,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC118344.1-3	chr19:40788615-40789072	NONHSAT066363

Variant related genes	Relation type
AKT2	TF binding region
MIR641	TF binding region
ENSG00000206925	Chromatin interaction
ENSG00000105219	Chromatin interaction
ENSG00000160392	Chromatin interaction
ENSG00000130758	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10402740	0.81[JPT][hapmap];0.86[MEX][hapmap]
rs10405207	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1129156	0.82[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap]
rs11668242	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12609706	0.86[ASN][1000 genomes]
rs12974529	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12981110	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2304184	0.82[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap]
rs2304189	0.89[CHB][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs339526	0.90[CHB][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap]
rs3730050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3730051	0.82[CEU][hapmap];0.80[CHB][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes]
rs4239504	0.82[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.93[MEX][hapmap]
rs4239506	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4257318	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4277441	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4332845	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4337402	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4490099	0.95[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4499338	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4558508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4802070	0.82[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap]
rs4802071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4802073	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4802074	0.82[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.80[TSI][hapmap]
rs4803320	0.82[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6508936	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7248338	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7249146	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.88[ASN][1000 genomes]
rs7250897	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7255581	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7257972	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7260106	0.85[ASN][1000 genomes]
rs7260517	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs748236	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7508604	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8100018	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs8102171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8104727	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8110888	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.85[ASN][1000 genomes]
rs969531	0.95[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9749283	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv2758499	chr19:40612420-40839520	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv2758761	chr19:40612420-40839520	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv911699	chr19:40691632-40816530	Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	esv1833489	chr19:40722123-40923908	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv1057052	chr19:40776128-40789766	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
7	esv1005660	chr19:40784738-40790835	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11880261	SYMPK	cis	cerebellum	SCAN
rs11880261	ERCC1	cis	parietal	SCAN
rs11880261	BLVRB	cis	multi-tissue	Pritchard
rs11880261	IGFL4	cis	parietal	SCAN
rs11880261	ZNF221	cis	parietal	SCAN
rs11880261	C19orf47	cis	lymphoblastoid	seeQTL
rs11880261	TMEM91	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40770000-40789600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:40770000-40789600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr19:40770200-40789600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr19:40770200-40790200	Weak transcription	Aorta	Aorta
5	chr19:40771400-40789400	Weak transcription	HUVEC	blood vessel
6	chr19:40779400-40789600	Enhancers	Left Ventricle	heart
7	chr19:40779800-40789800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr19:40782200-40789400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr19:40783000-40789600	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr19:40783200-40789200	Enhancers	Brain Cingulate Gyrus	brain
11	chr19:40783400-40790000	Enhancers	Right Atrium	heart
12	chr19:40783800-40790600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr19:40784400-40789000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr19:40785000-40789200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr19:40785200-40789200	Enhancers	NHDF-Ad	bronchial
16	chr19:40785200-40789600	Genic enhancers	Fetal Intestine Small	intestine
17	chr19:40785400-40788800	Enhancers	Ovary	ovary
18	chr19:40785800-40789000	Genic enhancers	K562	blood
19	chr19:40785800-40789600	Genic enhancers	Fetal Muscle Leg	muscle
20	chr19:40785800-40789600	Genic enhancers	Fetal Stomach	stomach
21	chr19:40786000-40790000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr19:40786200-40789400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr19:40786400-40789400	Genic enhancers	Fetal Muscle Trunk	muscle
24	chr19:40786400-40789600	Enhancers	Colon Smooth Muscle	Colon
25	chr19:40786400-40790200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr19:40786600-40789200	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr19:40786800-40788800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr19:40786800-40788800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr19:40786800-40789400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr19:40786800-40789400	Genic enhancers	Primary T cells fromperipheralblood	blood
31	chr19:40786800-40789800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr19:40787000-40788800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr19:40787000-40788800	Weak transcription	Primary hematopoietic stem cells	blood
34	chr19:40787000-40789000	Enhancers	Duodenum Mucosa	Duodenum
35	chr19:40787000-40789200	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr19:40787000-40789600	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr19:40787000-40789600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr19:40787000-40789600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr19:40787000-40790000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr19:40787000-40790000	Genic enhancers	Spleen	Spleen
41	chr19:40787200-40788800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr19:40787200-40788800	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr19:40787200-40788800	Weak transcription	HMEC	breast
44	chr19:40787200-40789200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr19:40787200-40789200	Strong transcription	Thymus	Thymus
46	chr19:40787200-40789400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr19:40787200-40789400	Genic enhancers	Dnd41	blood
48	chr19:40787200-40789600	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr19:40787200-40789800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr19:40787200-40790000	Weak transcription	Small Intestine	intestine

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