Variant report

Variant	rs11665867
Chromosome Location	chr19:41266479-41266480
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:41266374-41266896	K562	blood:	n/a	n/a
2	POLR2A	chr19:41266413-41267128	K562	blood:	n/a	n/a
3	POLR2A	chr19:41266185-41267314	GM12892	blood:	n/a	n/a
4	POLR2A	chr19:41266233-41267168	GM12892	blood:	n/a	n/a
5	POLR2A	chr19:41266295-41266842	A549	lung:	n/a	n/a
6	POLR2A	chr19:41266427-41266903	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr19:41265946-41267123	HepG2	liver:	n/a	n/a
8	POLR2A	chr19:41265920-41267445	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr19:41266285-41267261	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr19:41266420-41266615	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr19:41266219-41266847	K562	blood:	n/a	n/a
12	POLR2A	chr19:41266121-41267267	SK-N-MC	brain:	n/a	n/a
13	POLR2A	chr19:41266106-41267332	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:41265822..41267974-chr19:41269618..41272874,3	MCF-7	breast:
2	chr19:41260139..41263549-chr19:41263654..41270764,10	MCF-7	breast:
3	chr19:41265580..41267583-chr19:41282602..41284683,2	K562	blood:
4	chr19:41264656..41268852-chr19:41282370..41284831,5	K562	blood:
5	chr19:41263983..41267692-chr19:41276306..41279646,3	K562	blood:
6	chr19:41224657..41226437-chr19:41266206..41269077,2	MCF-7	breast:

No data

Variant related genes	Relation type
SNRPA	TF binding region
ENSG00000171570	Chromatin interaction
ENSG00000261857	Chromatin interaction
ENSG00000077312	Chromatin interaction
ENSG00000167578	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11665953	1.00[ASN][1000 genomes]
rs11666504	0.86[ASW][hapmap];0.93[CEU][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11667119	1.00[ASN][1000 genomes]
rs11667931	1.00[ASN][1000 genomes]
rs11668042	1.00[ASN][1000 genomes]
rs11668501	0.87[ASW][hapmap];0.96[LWK][hapmap]
rs11672227	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11672651	1.00[ASN][1000 genomes]
rs11673492	0.87[ASW][hapmap]
rs12975396	0.88[LWK][hapmap]
rs2077407	1.00[ASN][1000 genomes]
rs2279011	1.00[YRI][hapmap]
rs36012476	1.00[ASN][1000 genomes]
rs4435368	1.00[ASN][1000 genomes]
rs4624303	1.00[ASN][1000 genomes]
rs55652103	1.00[ASN][1000 genomes]
rs55658896	1.00[ASN][1000 genomes]
rs55723406	1.00[ASN][1000 genomes]
rs55856492	1.00[ASN][1000 genomes]
rs56041558	1.00[ASN][1000 genomes]
rs56140728	1.00[ASN][1000 genomes]
rs7253502	0.87[ASW][hapmap];0.92[LWK][hapmap]
rs7253575	1.00[ASN][1000 genomes]
rs7258772	1.00[ASN][1000 genomes]
rs7259121	1.00[ASN][1000 genomes]
rs73035918	1.00[ASN][1000 genomes]
rs73047051	1.00[ASN][1000 genomes]
rs73047068	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73047073	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73047085	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73047100	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73048915	1.00[ASN][1000 genomes]
rs73048925	1.00[ASN][1000 genomes]
rs8105009	0.87[ASW][hapmap];0.88[LWK][hapmap]
rs8106578	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	esv1802033	chr19:41256131-41284240	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	40 gene(s)	inside rSNPs	diseases
4	esv1801805	chr19:41256581-41284363	Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	37 gene(s)	inside rSNPs	diseases
5	nsv833832	chr19:41260363-41334597	Strong transcription Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11665867	C19orf73	cis	parietal	SCAN
rs11665867	STRN4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41258000-41283000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:41258800-41268400	Weak transcription	Psoas Muscle	Psoas
3	chr19:41259000-41275200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:41259200-41272800	Strong transcription	H1 Cell Line	embryonic stem cell
5	chr19:41260200-41266800	Genic enhancers	Spleen	Spleen
6	chr19:41260200-41272000	Strong transcription	H9 Cell Line	embryonic stem cell
7	chr19:41260400-41266600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:41260400-41271800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
9	chr19:41260600-41272400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr19:41260600-41272600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr19:41260600-41277200	Strong transcription	Fetal Brain Female	brain
12	chr19:41260800-41272200	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr19:41260800-41272200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr19:41260800-41272400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr19:41260800-41272400	Strong transcription	Brain Anterior Caudate	brain
16	chr19:41260800-41283200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr19:41261000-41271800	Strong transcription	HSMM	muscle
18	chr19:41261000-41272200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr19:41261000-41272200	Strong transcription	Muscle Satellite Cultured Cells	--
20	chr19:41261200-41272200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr19:41261200-41272200	Strong transcription	Fetal Lung	lung
22	chr19:41261200-41273000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr19:41261200-41273600	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr19:41261600-41267800	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr19:41261600-41269000	Strong transcription	Brain Hippocampus Middle	brain
26	chr19:41261600-41272000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
27	chr19:41261600-41272000	Strong transcription	Osteobl	bone
28	chr19:41261600-41272200	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr19:41261600-41272200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr19:41261600-41275000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr19:41261600-41275200	Strong transcription	Fetal Muscle Trunk	muscle
32	chr19:41261800-41272000	Strong transcription	Ovary	ovary
33	chr19:41261800-41272200	Strong transcription	Primary hematopoietic stem cells	blood
34	chr19:41261800-41272200	Strong transcription	NHLF	lung
35	chr19:41261800-41272400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr19:41261800-41272400	Strong transcription	Fetal Intestine Large	intestine
37	chr19:41261800-41272400	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr19:41261800-41272600	Strong transcription	Right Ventricle	heart
39	chr19:41261800-41276800	Strong transcription	Fetal Intestine Small	intestine
40	chr19:41261800-41278200	Strong transcription	Fetal Stomach	stomach
41	chr19:41261800-41282800	Weak transcription	Right Atrium	heart
42	chr19:41262000-41270000	Weak transcription	Fetal Heart	heart
43	chr19:41262000-41272200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr19:41262000-41272200	Strong transcription	K562	blood
45	chr19:41262000-41273400	Strong transcription	Brain Germinal Matrix	brain
46	chr19:41262000-41276200	Strong transcription	Thymus	Thymus
47	chr19:41262200-41273800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr19:41262400-41270400	Strong transcription	Fetal Thymus	thymus
49	chr19:41262400-41272400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr19:41262400-41273000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links