Variant report

Variant	rs11880977
Chromosome Location	chr19:42391079-42391080
allele	A/G
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:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:42390528..42393391-chr19:42425919..42428755,3	MCF-7	breast:
2	chr19:42385706..42396512-chr19:42423854..42433641,19	K562	blood:
3	chr19:42390140..42393678-chr19:42394261..42398306,6	K562	blood:
4	chr19:42389117..42392218-chr19:42417443..42420229,3	K562	blood:
5	chr19:42385318..42391505-chr19:42458040..42463569,9	MCF-7	breast:
6	chr19:42389371..42391920-chr19:42438453..42441265,2	MCF-7	breast:
7	chr19:42390499..42394130-chr19:42395488..42398499,5	MCF-7	breast:
8	chr19:42389117..42391614-chr19:42418078..42420063,2	K562	blood:
9	chr19:42387260..42389981-chr19:42390048..42391811,2	K562	blood:
10	chr19:42384855..42393410-chr19:42428364..42439251,22	K562	blood:
11	chr19:42390553..42393119-chr19:42395224..42396776,2	MCF-7	breast:
12	chr19:42389271..42392129-chr19:42772552..42774561,2	MCF-7	breast:
13	chr19:42389824..42391780-chr19:42439808..42442241,2	K562	blood:
14	chr19:42387951..42392334-chr19:42459610..42463737,7	MCF-7	breast:
15	chr19:42390344..42392993-chr19:42439270..42441134,2	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:
18	chr19:42390993..42392677-chr19:42461992..42463492,2	K562	blood:
19	chr19:42390448..42392513-chr19:42434205..42436040,2	MCF-7	breast:

No data

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

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

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];0.89[LWK][hapmap]
rs11878687	1.00[MEX][hapmap];0.82[YRI][hapmap]
rs11878734	1.00[CEU][hapmap]
rs11879437	1.00[CEU][hapmap];1.00[MEX][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes]
rs11879519	0.82[YRI][hapmap]
rs11881323	1.00[CEU][hapmap];0.91[YRI][hapmap]
rs11883018	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]
rs12104228	1.00[CEU][hapmap]
rs2288512	1.00[CEU][hapmap]
rs34537433	1.00[MEX][hapmap]
rs41303849	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41307029	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs717225	1.00[CEU][hapmap]
rs7253691	1.00[CEU][hapmap]
rs7255488	1.00[MEX][hapmap]
rs7260129	1.00[CEU][hapmap]
rs8112569	0.82[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	chr19:42388600-42391400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
2	chr19:42389000-42391200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr19:42389000-42391200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr19:42389000-42392400	Enhancers	Pancreas	Pancrea
5	chr19:42389000-42396000	Weak transcription	Aorta	Aorta
6	chr19:42389000-42396000	Weak transcription	Ovary	ovary
7	chr19:42389200-42391200	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr19:42389200-42391600	Enhancers	Fetal Heart	heart
9	chr19:42389200-42391600	Enhancers	Fetal Muscle Trunk	muscle
10	chr19:42389200-42391800	Enhancers	Adipose Nuclei	Adipose
11	chr19:42389200-42391800	Enhancers	Lung	lung
12	chr19:42389200-42392000	Genic enhancers	Spleen	Spleen
13	chr19:42389200-42392400	Enhancers	Fetal Intestine Large	intestine
14	chr19:42389200-42392600	Genic enhancers	Primary neutrophils fromperipheralblood	blood
15	chr19:42389200-42407200	Weak transcription	Fetal Kidney	kidney
16	chr19:42389200-42429200	Weak transcription	Right Atrium	heart
17	chr19:42389400-42391200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr19:42389400-42391200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr19:42389400-42391200	Enhancers	HepG2	liver
20	chr19:42389400-42391400	Enhancers	Brain Anterior Caudate	brain
21	chr19:42389400-42391600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr19:42389400-42391600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr19:42389400-42391600	Flanking Active TSS	Fetal Thymus	thymus
24	chr19:42389400-42391800	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr19:42389400-42392000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
26	chr19:42389400-42392000	Enhancers	Fetal Intestine Small	intestine
27	chr19:42389400-42392000	Weak transcription	NHLF	lung
28	chr19:42389400-42392200	Weak transcription	Fetal Brain Female	brain
29	chr19:42389400-42392400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr19:42389400-42392400	Enhancers	Gastric	stomach
31	chr19:42389400-42392600	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr19:42389400-42392800	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr19:42389400-42393000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr19:42389400-42393600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr19:42389400-42398200	Weak transcription	Colon Smooth Muscle	Colon
36	chr19:42389400-42402000	Weak transcription	Psoas Muscle	Psoas
37	chr19:42389400-42406000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:42389400-42411400	Weak transcription	Fetal Brain Male	brain
39	chr19:42389600-42391400	Weak transcription	Brain Germinal Matrix	brain
40	chr19:42389800-42391400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr19:42389800-42392000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
42	chr19:42389800-42392400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
43	chr19:42389800-42392800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
44	chr19:42389800-42393000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr19:42389800-42409000	Strong transcription	Fetal Stomach	stomach
46	chr19:42390000-42391600	Enhancers	Liver	Liver
47	chr19:42390000-42391800	Enhancers	Muscle Satellite Cultured Cells	--
48	chr19:42390000-42392200	Enhancers	Placenta Amnion	Placenta Amnion
49	chr19:42390000-42392200	Enhancers	Right Ventricle	heart
50	chr19:42390000-42392600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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