Variant report

Variant	rs11670882
Chromosome Location	chr19:19649748-19649749
allele	C/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	CTCF	chr19:19649700-19649850	GM12872	blood:	n/a	n/a
2	MAZ	chr19:19648707-19649977	IMR90	lung:	n/a	chr19:19649515-19649525 chr19:19649059-19649069
3	REST	chr19:19649497-19649845	H1-hESC	embryonic stem cell:	n/a	chr19:19649687-19649696 chr19:19649676-19649696
4	REST	chr19:19649497-19649894	ECC-1	luminal epithelium:	n/a	chr19:19649687-19649696 chr19:19649676-19649696
5	REST	chr19:19649491-19649823	SK-N-SH	brain:	n/a	chr19:19649687-19649696 chr19:19649676-19649696

No.	Distal block	Cell Line	Cell type
1	chr19:19647870..19650487-chr19:19773815..19776020,2	MCF-7	breast:
2	chr19:19648360..19650075-chr19:19737805..19740650,3	MCF-7	breast:
3	chr19:19625369..19628375-chr19:19648780..19652325,4	MCF-7	breast:
4	chr19:19649331..19652417-chr19:19771491..19776120,6	K562	blood:
5	chr19:19649600..19655493-chr19:19770960..19774805,7	K562	blood:
6	chr19:19625665..19627306-chr19:19648287..19650892,2	K562	blood:

Variant related genes	Relation type
CILP2	TF binding region
ENSG00000178093	Chromatin interaction
ENSG00000064547	Chromatin interaction
ENSG00000105726	Chromatin interaction
ENSG00000258674	Chromatin interaction
ENSG00000186010	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10221485	0.94[ASN][1000 genomes]
rs1036215	0.94[CEU][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes]
rs11085264	0.94[CEU][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes]
rs11668203	0.86[EUR][1000 genomes]
rs11669558	0.92[EUR][1000 genomes]
rs11669730	0.82[CEU][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes]
rs11670687	0.94[EUR][1000 genomes]
rs11670761	0.95[EUR][1000 genomes]
rs11670775	0.94[CEU][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes]
rs11671253	0.94[EUR][1000 genomes]
rs1560687	0.94[CEU][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs16996127	0.88[ASW][hapmap];0.94[CEU][hapmap];0.94[LWK][hapmap];0.88[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs17684164	0.94[CEU][hapmap];0.96[EUR][1000 genomes]
rs1865036	0.94[ASN][1000 genomes]
rs2060274	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs2060275	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs2304097	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2916070	0.94[CEU][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes]
rs2916072	0.86[EUR][1000 genomes]
rs2916075	0.86[EUR][1000 genomes]
rs2965179	0.83[EUR][1000 genomes]
rs2965181	0.83[EUR][1000 genomes]
rs2965184	0.94[CEU][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs2965186	0.93[CEU][hapmap];0.96[TSI][hapmap];0.80[EUR][1000 genomes]
rs2965190	0.90[TSI][hapmap]
rs2965195	0.94[CEU][hapmap];0.96[TSI][hapmap]
rs2965201	0.94[CEU][hapmap];0.96[TSI][hapmap]
rs34487417	0.81[EUR][1000 genomes]
rs34667451	0.94[EUR][1000 genomes]
rs45556231	0.95[EUR][1000 genomes]
rs45631651	0.95[EUR][1000 genomes]
rs4808204	0.94[EUR][1000 genomes]
rs4808205	0.95[EUR][1000 genomes]
rs4808206	0.94[CEU][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes]
rs4808951	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs4808958	0.81[EUR][1000 genomes]
rs4808962	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs4808968	0.94[CEU][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes]
rs4808969	0.95[EUR][1000 genomes]
rs4808970	0.94[EUR][1000 genomes]
rs55927782	0.95[EUR][1000 genomes]
rs56280531	0.94[EUR][1000 genomes]
rs56291054	0.81[EUR][1000 genomes]
rs56330647	0.96[EUR][1000 genomes]
rs57368710	0.94[ASN][1000 genomes]
rs58074958	0.86[EUR][1000 genomes]
rs61744761	0.92[EUR][1000 genomes]
rs7245689	0.96[EUR][1000 genomes]
rs7249319	0.94[ASN][1000 genomes]
rs7250233	0.94[CEU][hapmap];0.96[EUR][1000 genomes]
rs7252453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7256028	0.91[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs751857	0.84[TSI][hapmap];0.94[EUR][1000 genomes]
rs754256	0.94[CEU][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs756997	0.94[CEU][hapmap]
rs8100927	0.95[EUR][1000 genomes]
rs8101219	0.95[EUR][1000 genomes]
rs8102502	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8105642	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs8110171	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs8110250	0.94[CEU][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv911307	chr19:19631655-19657143	Bivalent Enhancer Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv911308	chr19:19631655-19663850	Strong transcription Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	esv1807343	chr19:19639345-19669570	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs11670882	LRRC25	cis	parietal	SCAN
rs11670882	GATAD2A	cis	parietal	SCAN
rs11670882	OCEL1	cis	parietal	SCAN
rs11670882	IL12RB1	cis	parietal	SCAN
rs11670882	JUND	cis	parietal	SCAN
rs11670882	DDX49	cis	cerebellum	SCAN
rs11670882	EDG4	cis	multi-tissue	Pritchard
rs11670882	LSM4	cis	cerebellum	SCAN
rs11670882	SF4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19630600-19651800	Weak transcription	A549	lung
2	chr19:19642200-19650600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr19:19643600-19675400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:19647800-19650000	Enhancers	Spleen	Spleen
5	chr19:19648000-19649800	Bivalent Enhancer	Fetal Intestine Large	intestine
6	chr19:19648000-19649800	Enhancers	Pancreas	Pancrea
7	chr19:19648200-19649800	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
8	chr19:19648200-19650000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
9	chr19:19648200-19650000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr19:19648200-19650000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
11	chr19:19648200-19650000	Bivalent Enhancer	Fetal Thymus	thymus
12	chr19:19648200-19650000	Enhancers	Lung	lung
13	chr19:19648200-19651400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
14	chr19:19648200-19651600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
15	chr19:19648400-19649800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
16	chr19:19648400-19649800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr19:19648400-19650000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
18	chr19:19648400-19650000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
19	chr19:19648400-19650200	Bivalent Enhancer	Placenta	Placenta
20	chr19:19648400-19651400	Bivalent Enhancer	Fetal Stomach	stomach
21	chr19:19648600-19649800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr19:19648600-19649800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
23	chr19:19648600-19649800	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr19:19648600-19649800	Bivalent Enhancer	Fetal Intestine Small	intestine
25	chr19:19648600-19649800	Bivalent Enhancer	Stomach Mucosa	stomach
26	chr19:19648600-19650000	Bivalent Enhancer	Primary T cells from cord blood	blood
27	chr19:19648600-19650000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr19:19648600-19650000	Bivalent Enhancer	Adipose Nuclei	Adipose
29	chr19:19648600-19650000	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
30	chr19:19648600-19650200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
31	chr19:19648800-19649800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
32	chr19:19648800-19649800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
33	chr19:19648800-19649800	Bivalent Enhancer	Fetal Lung	lung
34	chr19:19648800-19649800	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
35	chr19:19648800-19649800	Flanking Bivalent TSS/Enh	NHEK	skin
36	chr19:19648800-19650000	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr19:19648800-19650000	Bivalent Enhancer	Primary B cells from cord blood	blood
38	chr19:19648800-19650000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr19:19648800-19650200	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr19:19649000-19649800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
41	chr19:19649000-19649800	Enhancers	Left Ventricle	heart
42	chr19:19649000-19650000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr19:19649000-19650000	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
44	chr19:19649200-19649800	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr19:19649200-19649800	Flanking Bivalent TSS/Enh	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr19:19649200-19649800	Flanking Bivalent TSS/Enh	Colon Smooth Muscle	Colon
47	chr19:19649200-19649800	Bivalent Enhancer	Fetal Brain Male	brain
48	chr19:19649200-19649800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
49	chr19:19649200-19649800	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
50	chr19:19649200-19650000	Bivalent Enhancer	Esophagus	oesophagus

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