Variant report

Variant	rs10404589
Chromosome Location	chr19:43019863-43019864
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr19:43019600-43019938	GM12878	blood:	n/a	n/a
2	EP300	chr19:43019423-43020064	GM12878	blood:	n/a	n/a
3	RUNX3	chr19:43019566-43019915	GM12878	blood:	n/a	n/a
4	ZNF384	chr19:43019590-43019988	GM12878	blood:	n/a	n/a
5	BATF	chr19:43019663-43019875	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
CEACAM1	TF binding region

Extended variants
information (count: 104 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10401178	1.00[CEU][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10401428	1.00[EUR][1000 genomes]
rs10402853	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10403065	1.00[EUR][1000 genomes]
rs10405037	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10405152	1.00[CEU][hapmap]
rs10405179	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10405410	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10405942	1.00[EUR][1000 genomes]
rs10406227	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10408822	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10412074	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10412173	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs10412594	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10414396	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10415284	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10416108	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10418090	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10418997	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10419543	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10419561	1.00[EUR][1000 genomes]
rs10420773	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10422191	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10423227	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10423370	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10424206	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10425199	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10425666	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10426304	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11878991	1.00[CEU][hapmap]
rs11880554	1.00[CEU][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11880876	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11881583	1.00[CEU][hapmap]
rs11882225	1.00[EUR][1000 genomes]
rs11882291	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11882701	0.81[AFR][1000 genomes]
rs11883406	1.00[CEU][hapmap]
rs11883425	1.00[CEU][hapmap]
rs13343840	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13345272	1.00[EUR][1000 genomes]
rs13346522	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16975787	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16975799	1.00[CEU][hapmap];0.81[AFR][1000 genomes]
rs16975815	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16975862	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2051832	1.00[EUR][1000 genomes]
rs2051833	0.83[EUR][1000 genomes]
rs28403155	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28425201	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28433890	1.00[AMR][1000 genomes]
rs28473486	1.00[EUR][1000 genomes]
rs28588100	1.00[EUR][1000 genomes]
rs28602626	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28635141	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28660279	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41348545	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41381546	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41421250	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57018456	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58050143	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58162305	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs58702905	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs60747186	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61388144	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6509015	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6509019	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7246161	1.00[CEU][hapmap]
rs7246591	1.00[CEU][hapmap]
rs7247278	1.00[CEU][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7248907	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7249304	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7250501	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7252874	0.81[AFR][1000 genomes]
rs7253634	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7255271	1.00[EUR][1000 genomes]
rs7256226	1.00[EUR][1000 genomes]
rs7256850	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7258854	1.00[CEU][hapmap]
rs7259335	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73558492	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73558498	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73560408	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8101378	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8104731	0.81[AFR][1000 genomes]
rs8105525	1.00[CEU][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8106836	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8107720	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8108992	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8109086	0.96[AFR][1000 genomes]
rs8110904	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8110922	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8111171	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8111468	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs8112593	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8112915	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8113154	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8113448	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9749434	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9916999	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9917002	0.81[AFR][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:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:43002200-43025200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr19:43002400-43022400	Weak transcription	Lung	lung
3	chr19:43002800-43023000	Weak transcription	Gastric	stomach
4	chr19:43003200-43030600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr19:43003400-43028400	Weak transcription	Esophagus	oesophagus
6	chr19:43003400-43029400	Weak transcription	Small Intestine	intestine
7	chr19:43006200-43029800	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr19:43009200-43023200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:43010200-43024800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr19:43010800-43023000	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr19:43012200-43028200	Strong transcription	Liver	Liver
12	chr19:43013800-43032000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr19:43014600-43024400	Weak transcription	Fetal Stomach	stomach
14	chr19:43014800-43022000	Strong transcription	HepG2	liver
15	chr19:43015600-43023000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr19:43015600-43030800	Weak transcription	Left Ventricle	heart
17	chr19:43015800-43025400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr19:43016000-43032400	Weak transcription	Brain Anterior Caudate	brain
19	chr19:43016200-43023200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr19:43016400-43025000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr19:43016600-43022000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr19:43016600-43023200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr19:43016600-43023600	Weak transcription	Spleen	Spleen
24	chr19:43016600-43024200	Weak transcription	Colonic Mucosa	Colon
25	chr19:43016600-43024800	Weak transcription	Adipose Nuclei	Adipose
26	chr19:43016600-43029400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr19:43016600-43031800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr19:43017000-43025200	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr19:43017200-43024200	Weak transcription	Primary B cells from cord blood	blood
30	chr19:43017400-43031400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr19:43017800-43025600	Weak transcription	Primary B cells from peripheral blood	blood
32	chr19:43018200-43030400	Weak transcription	Rectal Smooth Muscle	rectum
33	chr19:43018600-43027200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr19:43019000-43023000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr19:43019000-43023000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr19:43019000-43029200	Weak transcription	Stomach Mucosa	stomach
37	chr19:43019400-43023000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr19:43019400-43023000	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr19:43019400-43027000	Weak transcription	Placenta	Placenta
40	chr19:43019600-43021600	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr19:43019600-43023000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr19:43019600-43023200	Weak transcription	Primary T cells from cord blood	blood
43	chr19:43019800-43020600	Genic enhancers	Primary neutrophils fromperipheralblood	blood
44	chr19:43019800-43021800	Weak transcription	Fetal Intestine Large	intestine
45	chr19:43019800-43022000	Weak transcription	Duodenum Mucosa	Duodenum
46	chr19:43019800-43022200	Weak transcription	Fetal Intestine Small	intestine

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