Variant report

Variant	rs10402677
Chromosome Location	chr19:43025170-43025171
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 114 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10084159	0.84[AMR][1000 genomes]
rs10401271	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs10402361	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10402401	0.85[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10403517	0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10403979	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10404402	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10404509	0.85[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10405445	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10405646	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10405906	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]
rs10407178	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10407576	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10410147	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10411165	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10411458	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10412463	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10413014	0.85[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs10413413	0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10414602	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10415564	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10416089	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10417418	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10417693	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10419378	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10420164	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10420796	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10421108	0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10421620	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10421881	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10422283	0.82[CHB][hapmap]
rs10422573	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10422987	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10423291	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10425241	0.82[AMR][1000 genomes]
rs10469271	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10469284	0.82[EUR][1000 genomes]
rs10469285	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10469286	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1076243	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11083659	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11665767	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11665870	0.94[ASW][hapmap];0.93[LWK][hapmap];0.89[MKK][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs11665935	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11666350	0.82[EUR][1000 genomes]
rs11666425	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11666835	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11666862	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11668009	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11668460	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11669892	0.87[ASN][1000 genomes]
rs11670316	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11671272	0.82[EUR][1000 genomes]
rs11671846	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11673645	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11673684	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11879306	0.96[ASN][1000 genomes]
rs11881517	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11882150	0.96[ASN][1000 genomes]
rs11882882	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12165114	0.82[CHB][hapmap]
rs12327586	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13343936	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs13346414	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16975865	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16975890	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1859341	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2267631	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28411988	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs28447294	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2883270	0.87[ASN][1000 genomes]
rs4080606	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4499340	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55641435	0.96[ASN][1000 genomes]
rs55850134	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56237547	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56978333	0.83[ASN][1000 genomes]
rs57902582	0.88[ASN][1000 genomes]
rs59525393	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60052467	0.80[AMR][1000 genomes]
rs60313903	0.96[ASN][1000 genomes]
rs60662795	0.94[ASN][1000 genomes]
rs6509016	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6509017	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6509020	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7247618	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7248042	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7248297	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7249411	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7253056	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7253209	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73562329	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8102439	0.94[ASW][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs8102519	0.88[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.89[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8103285	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8103891	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs8106083	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8106570	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs8107152	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8107254	0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs8107790	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs8108816	1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8108844	0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs8110766	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8110917	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8112156	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs851298	0.96[ASN][1000 genomes]
rs851301	0.96[ASN][1000 genomes]
rs851302	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9304604	0.88[ASW][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.89[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10402677	SEC1	cis	cerebellum	SCAN
rs10402677	KCNA7	cis	cerebellum	SCAN
rs10402677	PTOV1	cis	parietal	SCAN
rs10402677	PPP1R13L	cis	parietal	SCAN
rs10402677	ETHE1	cis	cerebellum	SCAN
rs10402677	ZNF223	cis	parietal	SCAN
rs10402677	FTL	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:43002200-43025200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr19:43003200-43030600	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr19:43003400-43028400	Weak transcription	Esophagus	oesophagus
4	chr19:43003400-43029400	Weak transcription	Small Intestine	intestine
5	chr19:43006200-43029800	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr19:43012200-43028200	Strong transcription	Liver	Liver
7	chr19:43013800-43032000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr19:43015600-43030800	Weak transcription	Left Ventricle	heart
9	chr19:43015800-43025400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr19:43016000-43032400	Weak transcription	Brain Anterior Caudate	brain
11	chr19:43016600-43029400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr19:43016600-43031800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr19:43017000-43025200	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr19:43017400-43031400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr19:43017800-43025600	Weak transcription	Primary B cells from peripheral blood	blood
16	chr19:43018200-43030400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr19:43018600-43027200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr19:43019000-43029200	Weak transcription	Stomach Mucosa	stomach
19	chr19:43019400-43027000	Weak transcription	Placenta	Placenta
20	chr19:43020400-43030400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr19:43021600-43026200	Strong transcription	Rectal Mucosa Donor 31	rectum
22	chr19:43021800-43027400	Strong transcription	Fetal Intestine Large	intestine
23	chr19:43022000-43026600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr19:43022000-43028200	Strong transcription	Duodenum Mucosa	Duodenum
25	chr19:43022000-43028400	Genic enhancers	HepG2	liver
26	chr19:43022200-43028600	Strong transcription	Fetal Intestine Small	intestine
27	chr19:43023000-43025400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr19:43023000-43026200	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr19:43023000-43026200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr19:43023000-43026400	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr19:43023000-43027800	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr19:43023200-43026200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr19:43023200-43026400	Strong transcription	Primary T cells from cord blood	blood
34	chr19:43023200-43027600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr19:43023200-43032400	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr19:43023400-43025400	Weak transcription	Gastric	stomach
37	chr19:43023600-43025200	Weak transcription	Lung	lung
38	chr19:43023600-43025600	Weak transcription	GM12878-XiMat	blood
39	chr19:43023600-43027200	Strong transcription	Spleen	Spleen
40	chr19:43023600-43029600	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr19:43023600-43031600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr19:43023600-43032200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr19:43023600-43033200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr19:43024000-43025400	Genic enhancers	Primary neutrophils fromperipheralblood	blood
45	chr19:43024200-43026200	Strong transcription	Primary B cells from cord blood	blood
46	chr19:43024400-43026200	Strong transcription	Fetal Stomach	stomach
47	chr19:43024400-43027000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr19:43024800-43025400	Enhancers	H1 Cell Line	embryonic stem cell
49	chr19:43024800-43025600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr19:43024800-43025600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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