Variant report

Variant	rs11666504
Chromosome Location	chr19:41309240-41309241
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:33)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:33 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BCL3	chr19:41309184-41310252	A549	lung:	n/a	chr19:41310003-41310011
2	POLR2A	chr19:41307677-41309301	HUVEC	blood vessel:	n/a	n/a
3	ELF1	chr19:41308450-41309500	GM12878	blood:	n/a	n/a
4	POLR2A	chr19:41307692-41309535	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr19:41308503-41309375	GM12892	blood:	n/a	n/a
6	WRNIP1	chr19:41309032-41309285	GM12878	blood:	n/a	n/a
7	POLR2A	chr19:41308529-41310616	HL-60	blood:	n/a	n/a
8	POLR2A	chr19:41308428-41312038	GM12892	blood:	n/a	n/a
9	POLR2A	chr19:41308572-41310464	GM18505	blood:	n/a	n/a
10	MAZ	chr19:41309224-41309299	HepG2	liver:	n/a	n/a
11	MAZ	chr19:41308764-41309257	K562	blood:	n/a	n/a
12	POLR2A	chr19:41308880-41317807	GM12891	blood:	n/a	n/a
13	POLR2A	chr19:41308407-41313533	K562	blood:	n/a	n/a
14	POLR2A	chr19:41307117-41318353	K562	blood:	n/a	n/a
15	POLR2A	chr19:41307663-41316128	GM12892	blood:	n/a	n/a
16	POLR2A	chr19:41307696-41309307	GM12891	blood:	n/a	n/a
17	POLR2A	chr19:41309087-41309434	GM12878	blood:	n/a	n/a
18	POLR2A	chr19:41307671-41311968	GM12878	blood:	n/a	n/a
19	POLR2A	chr19:41307768-41311357	K562	blood:	n/a	n/a
20	POLR2A	chr19:41308824-41309299	K562	blood:	n/a	n/a
21	POLR2A	chr19:41307876-41312060	HepG2	liver:	n/a	n/a
22	POLR2A	chr19:41307781-41314972	GM12891	blood:	n/a	n/a
23	POLR2A	chr19:41307556-41311130	H1-hESC	embryonic stem cell:	n/a	n/a
24	TCF12	chr19:41308895-41310320	A549	lung:	n/a	chr19:41310024-41310034
25	ZNF263	chr19:41309238-41309772	HEK293-T-REx	kidney:	n/a	chr19:41309338-41309347
26	POLR2A	chr19:41309057-41309276	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr19:41308487-41310598	GM12878	blood:	n/a	n/a
28	POLR2A	chr19:41308762-41311163	PFSK-1	brain:	n/a	n/a
29	POLR2A	chr19:41308432-41316432	K562	blood:	n/a	n/a
30	POLR2A	chr19:41308947-41309265	H1-neurons	neurons:	n/a	n/a
31	POLR2A	chr19:41307640-41313313	K562	blood:	n/a	n/a
32	POLR2A	chr19:41307839-41311076	GM12878	blood:	n/a	n/a
33	POLR2A	chr19:41308985-41316368	A549	lung:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:41220581..41222873-chr19:41307320..41309933,2	MCF-7	breast:
2	chr19:41282962..41284842-chr19:41308232..41310693,2	MCF-7	breast:
3	chr19:41254487..41259247-chr19:41302579..41309995,18	K562	blood:
4	chr19:41281718..41286533-chr19:41301356..41311124,20	K562	blood:
5	chr19:41220369..41226479-chr19:41305318..41310706,7	K562	blood:
6	chr19:41253776..41259894-chr19:41301950..41310086,19	MCF-7	breast:
7	chr19:41280805..41286068-chr19:41308324..41316733,13	K562	blood:
8	chr15:56951029..56951802-chr19:41309134..41309780,2	NB4	blood:
9	chr19:41115624..41118176-chr19:41306706..41309360,2	MCF-7	breast:
10	chr19:41253887..41263110-chr19:41303366..41316425,33	K562	blood:

No data

Variant related genes	Relation type
EGLN2	TF binding region
ENSG00000167578	Chromatin interaction
ENSG00000171570	Chromatin interaction
ENSG00000188493	Chromatin interaction
ENSG00000261857	Chromatin interaction
ENSG00000086544	Chromatin interaction
ENSG00000090006	Chromatin interaction
ENSG00000123815	Chromatin interaction
ENSG00000077312	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11665867	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]
rs11665953	1.00[ASN][1000 genomes]
rs11667119	1.00[ASN][1000 genomes]
rs11667931	1.00[ASN][1000 genomes]
rs11668042	1.00[ASN][1000 genomes]
rs11672227	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2077407	1.00[ASN][1000 genomes]
rs36012476	1.00[ASN][1000 genomes]
rs4435368	1.00[ASN][1000 genomes]
rs4624303	1.00[ASN][1000 genomes]
rs55652103	1.00[ASN][1000 genomes]
rs55723406	1.00[ASN][1000 genomes]
rs55856492	1.00[ASN][1000 genomes]
rs56041558	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56140728	1.00[ASN][1000 genomes]
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	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73047073	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73047085	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73047100	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73048915	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73048925	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	esv2758500	chr19:41291627-41546068	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv2758762	chr19:41291627-41546068	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1066637	chr19:41309211-41597896	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11666504	SNORD33	cis	cerebellum	SCAN
rs11666504	SNORD32A	cis	cerebellum	SCAN
rs11666504	C19orf73	cis	parietal	SCAN
rs11666504	STRN4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41305800-41316200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr19:41306000-41310400	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
3	chr19:41306000-41311800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr19:41306200-41309400	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
5	chr19:41306200-41309600	Transcr. at gene 5' and 3'	Fetal Adrenal Gland	Adrenal Gland
6	chr19:41306200-41309800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
7	chr19:41306200-41309800	Transcr. at gene 5' and 3'	Dnd41	blood
8	chr19:41306200-41310200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr19:41306200-41311200	Transcr. at gene 5' and 3'	Brain Germinal Matrix	brain
10	chr19:41306200-41313200	Enhancers	Fetal Heart	heart
11	chr19:41306400-41309800	Genic enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr19:41306400-41310000	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
13	chr19:41306400-41311200	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
14	chr19:41306400-41313600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr19:41306400-41313800	Genic enhancers	Fetal Thymus	thymus
16	chr19:41306400-41316200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr19:41306400-41316800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr19:41306600-41309600	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
19	chr19:41306600-41310000	Transcr. at gene 5' and 3'	Brain Dorsolateral Prefrontal Cortex	brain
20	chr19:41306600-41310200	Transcr. at gene 5' and 3'	Brain Anterior Caudate	brain
21	chr19:41306600-41310400	Genic enhancers	H1 Cell Line	embryonic stem cell
22	chr19:41306600-41311200	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
23	chr19:41306600-41311800	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr19:41306600-41312400	Genic enhancers	Fetal Muscle Trunk	muscle
25	chr19:41306600-41314000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr19:41306600-41314800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr19:41306800-41310600	Genic enhancers	Primary hematopoietic stem cells	blood
28	chr19:41306800-41311200	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr19:41306800-41312200	Weak transcription	HSMMtube	muscle
30	chr19:41306800-41313400	Genic enhancers	Gastric	stomach
31	chr19:41307000-41309800	Transcr. at gene 5' and 3'	K562	blood
32	chr19:41307000-41312400	Enhancers	Small Intestine	intestine
33	chr19:41307000-41313400	Genic enhancers	Sigmoid Colon	Sigmoid Colon
34	chr19:41307000-41315800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr19:41307200-41311200	Genic enhancers	Thymus	Thymus
36	chr19:41307200-41312400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
37	chr19:41307400-41309800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr19:41307400-41311600	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr19:41307600-41309600	Genic enhancers	Hela-S3	cervix
40	chr19:41307800-41309400	Flanking Active TSS	Colon Smooth Muscle	Colon
41	chr19:41307800-41309600	Flanking Active TSS	HUVEC	blood vessel
42	chr19:41307800-41309800	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr19:41307800-41310400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr19:41307800-41310400	Transcr. at gene 5' and 3'	Brain Cingulate Gyrus	brain
45	chr19:41307800-41310400	Flanking Active TSS	HepG2	liver
46	chr19:41307800-41311000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr19:41307800-41311800	Genic enhancers	HUES64 Cell Line	embryonic stem cell
48	chr19:41307800-41311800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
49	chr19:41308000-41310000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
50	chr19:41308000-41311400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--

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