Variant report

Variant	rs10406800
Chromosome Location	chr19:43013760-43013761
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CXCL17-3	chr19:43011547-43014396	refGeneNc_4167_NR_033747

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10401224	0.86[YRI][hapmap]
rs10402697	1.00[EUR][1000 genomes]
rs10403856	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10404650	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10407155	1.00[TSI][hapmap]
rs10407842	1.00[AMR][1000 genomes]
rs10408986	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10409428	0.86[YRI][hapmap]
rs10409433	1.00[AMR][1000 genomes]
rs10410129	1.00[AMR][1000 genomes]
rs10410174	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10410653	1.00[AMR][1000 genomes]
rs10411498	1.00[ASW][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];1.00[AMR][1000 genomes]
rs10411565	1.00[EUR][1000 genomes]
rs10411908	1.00[AMR][1000 genomes]
rs10413484	1.00[AMR][1000 genomes]
rs10414502	1.00[EUR][1000 genomes]
rs10414695	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10415759	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10416535	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10417606	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10418102	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10418312	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10418988	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10420327	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10421331	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10421409	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs10421857	0.93[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10421902	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10422301	1.00[AMR][1000 genomes]
rs10423959	1.00[TSI][hapmap]
rs10423978	1.00[TSI][hapmap]
rs10425003	1.00[AMR][1000 genomes]
rs10426284	1.00[AMR][1000 genomes]
rs10469287	1.00[EUR][1000 genomes]
rs11878183	1.00[EUR][1000 genomes]
rs11878207	0.93[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11879211	1.00[EUR][1000 genomes]
rs11880356	0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs13343322	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs13343388	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13343719	1.00[AMR][1000 genomes]
rs13343761	1.00[ASW][hapmap];1.00[AMR][1000 genomes]
rs13343834	1.00[AMR][1000 genomes]
rs13343966	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13346831	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13346879	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2229614	1.00[ASW][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28402882	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28463673	1.00[AMR][1000 genomes]
rs28469564	1.00[AMR][1000 genomes]
rs28474957	1.00[AMR][1000 genomes]
rs28483598	1.00[AMR][1000 genomes]
rs28496975	1.00[AMR][1000 genomes]
rs28545051	1.00[EUR][1000 genomes]
rs28657829	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28663042	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28675764	1.00[AMR][1000 genomes]
rs28686771	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28699037	1.00[AMR][1000 genomes]
rs33919763	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35707383	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs36089262	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs41407146	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41446245	1.00[EUR][1000 genomes]
rs59870753	1.00[AMR][1000 genomes]
rs60950516	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7246232	1.00[ASW][hapmap];0.92[LWK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7248473	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes]
rs7248543	1.00[EUR][1000 genomes]
rs7254853	1.00[AMR][1000 genomes]
rs7255343	1.00[AMR][1000 genomes]
rs7258727	0.93[YRI][hapmap];1.00[AMR][1000 genomes]
rs7258854	1.00[TSI][hapmap]
rs73552879	1.00[AMR][1000 genomes]
rs73558432	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73560411	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8099885	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs8109258	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs8111527	1.00[EUR][1000 genomes]
rs9304602	1.00[AMR][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	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
2	esv2422471	chr19:42733141-43669485	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
3	esv2422468	chr19:42991289-43669027	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1057390	chr19:43003323-43173028	Enhancers Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:43002200-43015000	Weak transcription	Spleen	Spleen
2	chr19:43002200-43025200	Weak transcription	Primary hematopoietic stem cells	blood
3	chr19:43002400-43022400	Weak transcription	Lung	lung
4	chr19:43002800-43014800	Weak transcription	Adipose Nuclei	Adipose
5	chr19:43002800-43014800	Weak transcription	Left Ventricle	heart
6	chr19:43002800-43023000	Weak transcription	Gastric	stomach
7	chr19:43003200-43014600	Weak transcription	Primary B cells from cord blood	blood
8	chr19:43003200-43030600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr19:43003400-43014600	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr19:43003400-43015200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr19:43003400-43019000	Weak transcription	Placenta	Placenta
12	chr19:43003400-43028400	Weak transcription	Esophagus	oesophagus
13	chr19:43003400-43029400	Weak transcription	Small Intestine	intestine
14	chr19:43003600-43015000	Weak transcription	Colonic Mucosa	Colon
15	chr19:43003600-43015600	Weak transcription	Brain Anterior Caudate	brain
16	chr19:43003800-43015000	Weak transcription	Fetal Intestine Small	intestine
17	chr19:43004000-43014600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr19:43004600-43015000	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr19:43006200-43029800	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr19:43006400-43014600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr19:43008000-43014600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr19:43009200-43023200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr19:43010200-43024800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr19:43010800-43014400	Genic enhancers	Primary neutrophils fromperipheralblood	blood
25	chr19:43010800-43015000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr19:43010800-43023000	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr19:43011000-43015000	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr19:43011000-43015000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr19:43011600-43014600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr19:43011800-43013800	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr19:43012200-43028200	Strong transcription	Liver	Liver
32	chr19:43012600-43016200	Enhancers	GM12878-XiMat	blood
33	chr19:43012600-43016600	Strong transcription	Primary T cells from cord blood	blood
34	chr19:43012600-43017800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr19:43012800-43013800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr19:43012800-43015000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr19:43012800-43016000	Strong transcription	Fetal Intestine Large	intestine
38	chr19:43012800-43016200	Weak transcription	Right Ventricle	heart
39	chr19:43012800-43016400	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr19:43013000-43015000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr19:43013000-43016600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr19:43013000-43016600	Strong transcription	Duodenum Mucosa	Duodenum
43	chr19:43013200-43016400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr19:43013200-43016400	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr19:43013400-43014800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr19:43013400-43015000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr19:43013400-43015200	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr19:43013400-43015200	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr19:43013400-43016200	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr19:43013400-43016400	Weak transcription	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links