Variant report

Variant	rs11883018
Chromosome Location	chr19:42390324-42390325
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:42389226..42390893-chr19:42441627..42443907,2	MCF-7	breast:
2	chr19:42385735..42391033-chr19:42460351..42463651,6	K562	blood:
3	chr19:42385706..42396512-chr19:42423854..42433641,19	K562	blood:
4	chr19:42390140..42393678-chr19:42394261..42398306,6	K562	blood:
5	chr19:42389117..42392218-chr19:42417443..42420229,3	K562	blood:
6	chr19:42385318..42391505-chr19:42458040..42463569,9	MCF-7	breast:
7	chr19:42389371..42391920-chr19:42438453..42441265,2	MCF-7	breast:
8	chr19:42388358..42390538-chr19:42579521..42581745,2	MCF-7	breast:
9	chr19:42389117..42391614-chr19:42418078..42420063,2	K562	blood:
10	chr19:42387260..42389981-chr19:42390048..42391811,2	K562	blood:
11	chr19:42384855..42393410-chr19:42428364..42439251,22	K562	blood:
12	chr19:42389271..42392129-chr19:42772552..42774561,2	MCF-7	breast:
13	chr19:42386109..42390387-chr19:42411996..42416642,6	K562	blood:
14	chr19:42389824..42391780-chr19:42439808..42442241,2	K562	blood:
15	chr19:42387951..42392334-chr19:42459610..42463737,7	MCF-7	breast:
16	chr19:42388986..42391635-chr2:199208235..199210709,2	MCF-7	breast:
17	chr19:42362804..42368897-chr19:42386582..42393421,16	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000105732	Chromatin interaction
ENSG00000076928	Chromatin interaction
ENSG00000105372	Chromatin interaction
ENSG00000268041	Chromatin interaction
ENSG00000079432	Chromatin interaction
ENSG00000105404	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10414811	1.00[CEU][hapmap]
rs10417495	1.00[CEU][hapmap]
rs10419314	1.00[CEU][hapmap]
rs11083638	1.00[CEU][hapmap]
rs11083640	1.00[CEU][hapmap]
rs11878687	0.90[YRI][hapmap]
rs11878734	1.00[CEU][hapmap]
rs11879437	1.00[CEU][hapmap];0.95[LWK][hapmap];0.92[MKK][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes]
rs11879519	0.90[YRI][hapmap]
rs11880977	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11881323	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs12104228	1.00[CEU][hapmap]
rs2288512	1.00[CEU][hapmap]
rs41303849	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41307029	1.00[EUR][1000 genomes]
rs717225	1.00[CEU][hapmap]
rs7253691	1.00[CEU][hapmap]
rs7260129	1.00[CEU][hapmap]
rs8112569	0.90[YRI][hapmap]
rs8113686	1.00[CEU][hapmap]
rs9653098	1.00[CEU][hapmap]
rs9989667	1.00[CEU][hapmap]

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	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv1061878	chr19:42325490-42416056	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv911776	chr19:42343526-42416056	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv911777	chr19:42357455-42521108	Bivalent/Poised TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
6	nsv911778	chr19:42358362-42416056	Strong transcription Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42387600-42390400	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr19:42388600-42391400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
3	chr19:42389000-42390400	Transcr. at gene 5' and 3'	Thymus	Thymus
4	chr19:42389000-42390800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
5	chr19:42389000-42390800	Weak transcription	Esophagus	oesophagus
6	chr19:42389000-42391000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr19:42389000-42391200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr19:42389000-42391200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr19:42389000-42392400	Enhancers	Pancreas	Pancrea
10	chr19:42389000-42396000	Weak transcription	Aorta	Aorta
11	chr19:42389000-42396000	Weak transcription	Ovary	ovary
12	chr19:42389200-42390400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr19:42389200-42390400	Enhancers	Fetal Muscle Leg	muscle
14	chr19:42389200-42390600	Genic enhancers	Primary B cells from peripheral blood	blood
15	chr19:42389200-42390800	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr19:42389200-42391000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr19:42389200-42391000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr19:42389200-42391000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr19:42389200-42391000	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr19:42389200-42391000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr19:42389200-42391000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr19:42389200-42391000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr19:42389200-42391000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr19:42389200-42391200	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr19:42389200-42391600	Enhancers	Fetal Heart	heart
26	chr19:42389200-42391600	Enhancers	Fetal Muscle Trunk	muscle
27	chr19:42389200-42391800	Enhancers	Adipose Nuclei	Adipose
28	chr19:42389200-42391800	Enhancers	Lung	lung
29	chr19:42389200-42392000	Genic enhancers	Spleen	Spleen
30	chr19:42389200-42392400	Enhancers	Fetal Intestine Large	intestine
31	chr19:42389200-42392600	Genic enhancers	Primary neutrophils fromperipheralblood	blood
32	chr19:42389200-42407200	Weak transcription	Fetal Kidney	kidney
33	chr19:42389200-42429200	Weak transcription	Right Atrium	heart
34	chr19:42389400-42390400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr19:42389400-42390400	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr19:42389400-42390400	Weak transcription	Brain Angular Gyrus	brain
37	chr19:42389400-42390400	Weak transcription	Brain Cingulate Gyrus	brain
38	chr19:42389400-42390400	Enhancers	Duodenum Mucosa	Duodenum
39	chr19:42389400-42390400	Enhancers	Left Ventricle	heart
40	chr19:42389400-42390400	Weak transcription	Rectal Smooth Muscle	rectum
41	chr19:42389400-42390400	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr19:42389400-42390400	Weak transcription	HSMMtube	muscle
43	chr19:42389400-42390400	Weak transcription	Osteobl	bone
44	chr19:42389400-42390600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr19:42389400-42390600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr19:42389400-42390600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr19:42389400-42390600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr19:42389400-42390800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr19:42389400-42390800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr19:42389400-42390800	Enhancers	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links