Variant report

Variant	rs10405906
Chromosome Location	chr19:43013394-43013395
allele	A/G
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: 75 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10084159	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10401271	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10402361	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10402677	0.94[ASW][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10403517	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10403979	0.80[EUR][1000 genomes]
rs10405445	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10405646	0.87[AMR][1000 genomes]
rs10407576	0.88[CEU][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10412463	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10413413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10415564	0.80[AMR][1000 genomes]
rs10416089	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10417418	0.80[AMR][1000 genomes]
rs10417693	0.80[AMR][1000 genomes]
rs10419378	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10420796	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10421108	0.86[AMR][1000 genomes]
rs10422987	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10469271	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10469284	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10469286	0.88[CEU][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1076243	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11083659	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11665870	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11665935	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11666350	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666835	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11666862	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11668599	1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11671272	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11671846	1.00[GIH][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs11673645	1.00[GIH][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs11879306	0.88[EUR][1000 genomes]
rs11881517	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11882150	0.88[EUR][1000 genomes]
rs12611218	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13343936	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16975789	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16975865	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16975890	0.83[EUR][1000 genomes]
rs1859341	0.80[AMR][1000 genomes]
rs2267631	0.88[CEU][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs28411988	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28447294	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4080606	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4499340	0.80[AMR][1000 genomes]
rs55850134	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56237547	0.80[EUR][1000 genomes]
rs60313903	0.85[EUR][1000 genomes]
rs6509016	0.84[AFR][1000 genomes]
rs6509020	0.80[EUR][1000 genomes]
rs7248297	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7253056	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7253209	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8102439	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8102519	0.83[ASW][hapmap];0.88[CEU][hapmap];0.89[MEX][hapmap];0.91[MKK][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8103285	0.94[ASW][hapmap];0.88[CEU][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8103891	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8106083	0.80[AMR][1000 genomes]
rs8106570	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8107152	0.88[ASW][hapmap];0.88[CEU][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8107254	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8107790	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8108844	0.89[YRI][hapmap]
rs8110917	0.80[EUR][1000 genomes]
rs8112156	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs851298	0.85[EUR][1000 genomes]
rs851301	0.88[EUR][1000 genomes]
rs851302	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9304604	0.82[ASW][hapmap];0.89[MEX][hapmap];0.88[MKK][hapmap];0.93[YRI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10405906	ETHE1	cis	cerebellum	SCAN
rs10405906	KCNA7	cis	cerebellum	SCAN
rs10405906	PTOV1	cis	parietal	SCAN
rs10405906	KLK8	cis	parietal	SCAN
rs10405906	PPP1R13L	cis	parietal	SCAN
rs10405906	FTL	cis	cerebellum	SCAN
rs10405906	ZNF223	cis	parietal	SCAN
rs10405906	SEC1	cis	cerebellum	SCAN

Chromatin state (count:54 , 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	chr19:43003000-43013400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr19:43003200-43014600	Weak transcription	Primary B cells from cord blood	blood
9	chr19:43003200-43030600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr19:43003400-43014600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr19:43003400-43015200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr19:43003400-43019000	Weak transcription	Placenta	Placenta
13	chr19:43003400-43028400	Weak transcription	Esophagus	oesophagus
14	chr19:43003400-43029400	Weak transcription	Small Intestine	intestine
15	chr19:43003600-43015000	Weak transcription	Colonic Mucosa	Colon
16	chr19:43003600-43015600	Weak transcription	Brain Anterior Caudate	brain
17	chr19:43003800-43015000	Weak transcription	Fetal Intestine Small	intestine
18	chr19:43004000-43014600	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr19:43004600-43015000	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr19:43006200-43029800	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr19:43006400-43014600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr19:43008000-43014600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr19:43009200-43023200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr19:43010200-43024800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr19:43010800-43014400	Genic enhancers	Primary neutrophils fromperipheralblood	blood
26	chr19:43010800-43015000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr19:43010800-43023000	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr19:43011000-43015000	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr19:43011000-43015000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr19:43011600-43014600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr19:43011800-43013800	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr19:43012200-43028200	Strong transcription	Liver	Liver
33	chr19:43012400-43013400	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr19:43012400-43013600	Strong transcription	HepG2	liver
35	chr19:43012600-43013600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr19:43012600-43016200	Enhancers	GM12878-XiMat	blood
37	chr19:43012600-43016600	Strong transcription	Primary T cells from cord blood	blood
38	chr19:43012600-43017800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr19:43012800-43013400	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr19:43012800-43013600	Enhancers	Primary B cells from peripheral blood	blood
41	chr19:43012800-43013800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr19:43012800-43015000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr19:43012800-43016000	Strong transcription	Fetal Intestine Large	intestine
44	chr19:43012800-43016200	Weak transcription	Right Ventricle	heart
45	chr19:43012800-43016400	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr19:43013000-43013400	Enhancers	H1 Cell Line	embryonic stem cell
47	chr19:43013000-43013400	Enhancers	H9 Cell Line	embryonic stem cell
48	chr19:43013000-43013400	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr19:43013000-43015000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr19:43013000-43016600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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