Variant report

Variant	rs11883412
Chromosome Location	chr19:42688687-42688688
allele	G/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:12)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:42636977..42638186-chr19:42688284..42689046,3	MCF-7	breast:
2	chr19:42686573..42689269-chr19:42737459..42739419,2	MCF-7	breast:
3	chr19:42687341..42690027-chr19:42800548..42802977,2	K562	blood:
4	chr19:42612768..42613292-chr19:42688394..42689113,3	MCF-7	breast:
5	chr19:42687399..42690060-chr19:42770420..42772705,2	K562	blood:
6	chr19:42636571..42637932-chr19:42687904..42689192,14	MCF-7	breast:
7	chr19:42636828..42638293-chr19:42687653..42689156,13	K562	blood:
8	chr19:42620217..42621071-chr19:42688179..42688986,2	K562	blood:
9	chr19:42612418..42613472-chr19:42688181..42689150,6	K562	blood:
10	chr19:42637295..42639499-chr19:42687538..42690053,2	K562	blood:
11	chr19:42687243..42689479-chr19:42729926..42732337,2	MCF-7	breast:
12	chr19:42612392..42613330-chr19:42688089..42689604,8	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DEDD2-3	chr19:42688588-42688787	l_1694_chr19:42679914-42689519_brain

No data

Variant related genes	Relation type
ENSG00000266226	Chromatin interaction
ENSG00000079432	Chromatin interaction
ENSG00000254887	Chromatin interaction
ENSG00000028277	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10407506	0.86[CHD][hapmap];0.80[LWK][hapmap];0.83[YRI][hapmap]
rs10410185	0.82[CHB][hapmap]
rs10410198	0.82[CHB][hapmap]
rs10410698	0.82[CHB][hapmap]
rs10500285	0.86[CHD][hapmap];0.96[GIH][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11878620	0.81[ASW][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];0.80[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs11880124	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1206009	0.82[CHB][hapmap]
rs1206027	0.82[CHB][hapmap]
rs1206029	0.82[CHB][hapmap]
rs1206033	0.82[CHB][hapmap]
rs1206038	0.82[CHB][hapmap]
rs1206040	0.82[CHB][hapmap]
rs1206041	0.82[CHB][hapmap]
rs1206044	0.82[CHB][hapmap]
rs12232804	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1613100	0.82[CHB][hapmap]
rs1654623	0.82[CHB][hapmap]
rs1676211	0.82[CHB][hapmap]
rs1676217	0.82[CHB][hapmap]
rs1676221	0.82[CHB][hapmap]
rs1676222	0.82[CHB][hapmap]
rs1685565	0.82[CHB][hapmap]
rs16975663	0.83[ASW][hapmap];0.90[CEU][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.94[LWK][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap]
rs16975684	0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17270057	0.85[EUR][1000 genomes]
rs17270169	0.85[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17342067	0.80[EUR][1000 genomes]
rs17342179	0.85[EUR][1000 genomes]
rs17342284	0.85[CHB][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17750207	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2217342	0.87[TSI][hapmap]
rs2267630	0.82[CHB][hapmap]
rs2302485	0.89[GIH][hapmap];0.80[MEX][hapmap]
rs2303652	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2537697	0.82[CHB][hapmap]
rs2615614	0.82[CHB][hapmap]
rs28621009	0.82[CHB][hapmap]
rs3745231	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3745233	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3810148	0.82[CHB][hapmap]
rs3810151	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs3826705	0.85[CHD][hapmap];0.96[GIH][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes]
rs4141062	0.82[CHB][hapmap];0.89[GIH][hapmap];0.80[MEX][hapmap]
rs443239	0.86[CHD][hapmap];0.96[TSI][hapmap]
rs454150	0.83[ASW][hapmap];0.81[CEU][hapmap];0.85[CHD][hapmap];0.94[LWK][hapmap];0.82[MKK][hapmap];0.96[TSI][hapmap];0.81[YRI][hapmap]
rs4803520	0.96[TSI][hapmap]
rs57938324	0.80[AFR][1000 genomes]
rs59099214	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62119628	0.84[ASN][1000 genomes]
rs7248379	0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7251466	0.86[CHD][hapmap];0.96[TSI][hapmap]
rs7253767	0.80[EUR][1000 genomes]
rs7253791	0.80[EUR][1000 genomes]
rs7253915	0.80[EUR][1000 genomes]
rs73932877	0.98[ASN][1000 genomes]
rs741070	0.82[CHB][hapmap]
rs8108096	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8182491	0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs851296	0.82[CHB][hapmap]
rs899661	0.96[TSI][hapmap]
rs9636121	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
3	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
4	nsv911782	chr19:42514712-42931004	Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
5	esv1794508	chr19:42580026-42791462	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
6	nsv1055554	chr19:42619671-42821642	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
7	nsv833833	chr19:42657276-42783122	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
8	nsv526186	chr19:42676481-43203507	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42681800-42703600	Weak transcription	Right Atrium	heart
2	chr19:42686000-42690200	Enhancers	Primary B cells from cord blood	blood
3	chr19:42686000-42691200	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr19:42686600-42690800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr19:42687200-42689400	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr19:42687200-42690600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr19:42687400-42690200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr19:42687800-42690000	Enhancers	Primary B cells from peripheral blood	blood
9	chr19:42687800-42690400	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr19:42688000-42688800	Enhancers	Monocytes-CD14+_RO01746	blood
11	chr19:42688000-42690800	Enhancers	Primary T cells fromperipheralblood	blood
12	chr19:42688000-42691000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr19:42688200-42689000	Enhancers	H1 Cell Line	embryonic stem cell
14	chr19:42688200-42689000	Enhancers	H9 Cell Line	embryonic stem cell
15	chr19:42688200-42689000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr19:42688200-42689200	Enhancers	HSMMtube	muscle
17	chr19:42688200-42689800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr19:42688200-42689800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr19:42688200-42689800	Enhancers	Duodenum Mucosa	Duodenum
20	chr19:42688200-42689800	Enhancers	HSMM	muscle
21	chr19:42688200-42690000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr19:42688200-42690200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr19:42688200-42690200	Enhancers	Primary T cells from cord blood	blood
24	chr19:42688200-42690200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr19:42688200-42690200	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr19:42688200-42690200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr19:42688200-42690200	Enhancers	Dnd41	blood
28	chr19:42688200-42691000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr19:42688200-42691000	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr19:42688400-42689000	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr19:42688400-42689000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr19:42688400-42689000	Enhancers	Fetal Intestine Small	intestine
33	chr19:42688400-42689000	Enhancers	Rectal Mucosa Donor 29	rectum
34	chr19:42688400-42689200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr19:42688400-42689600	Enhancers	NH-A	brain
36	chr19:42688400-42689800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr19:42688400-42689800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr19:42688400-42689800	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr19:42688400-42689800	Enhancers	Stomach Mucosa	stomach
40	chr19:42688400-42689800	Enhancers	HMEC	breast
41	chr19:42688400-42689800	Enhancers	NHEK	skin
42	chr19:42688400-42689800	Enhancers	Osteobl	bone
43	chr19:42688400-42690000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr19:42688400-42690200	Enhancers	Primary hematopoietic stem cells	blood
45	chr19:42688400-42690200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr19:42688400-42690200	Enhancers	Thymus	Thymus
47	chr19:42688400-42690200	Enhancers	Spleen	Spleen
48	chr19:42688400-42690800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr19:42688400-42690800	Enhancers	Fetal Thymus	thymus
50	chr19:42688600-42688800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links