Variant report

Variant	rs855640
Chromosome Location	chr19:38580344-38580345
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10403716	0.87[EUR][1000 genomes]
rs10405667	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10412762	0.87[CEU][hapmap];0.81[JPT][hapmap]
rs10413751	0.82[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs10414433	0.82[CEU][hapmap]
rs10420506	0.81[JPT][hapmap]
rs10422665	0.87[CEU][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1568975	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1614979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1622409	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1625884	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1654349	0.82[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs1654355	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1654357	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1654358	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1654359	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1654365	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.82[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1654367	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1725461	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1725473	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1725475	0.82[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs1725479	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1725506	0.80[ASN][1000 genomes]
rs1725512	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2005054	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2082442	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2082443	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28412601	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28581256	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3760882	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3810356	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4802233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802239	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4802247	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4802256	0.87[CEU][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap]
rs4803786	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4803800	0.85[EUR][1000 genomes]
rs4803801	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4803802	0.85[EUR][1000 genomes]
rs4803803	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4803809	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4803810	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4803828	0.81[JPT][hapmap]
rs4803829	0.81[JPT][hapmap]
rs56166457	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56293547	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58152231	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59185302	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59579475	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59924887	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61388128	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs705505	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71179415	0.86[EUR][1000 genomes]
rs7248428	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7250034	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs729625	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs729626	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs735615	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs754123	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8105468	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8106266	0.84[EUR][1000 genomes]
rs855598	0.89[ASN][1000 genomes]
rs855599	0.88[ASN][1000 genomes]
rs855601	0.83[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs855602	0.86[EUR][1000 genomes]
rs855603	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs855619	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs855621	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs855623	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs855624	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs855625	0.86[EUR][1000 genomes]
rs855627	0.89[EUR][1000 genomes]
rs855630	0.92[EUR][1000 genomes]
rs855631	0.82[EUR][1000 genomes]
rs855633	0.94[CEU][hapmap];0.83[CHB][hapmap];0.90[EUR][1000 genomes]
rs855634	0.90[EUR][1000 genomes]
rs855636	0.82[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs855637	0.82[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs855638	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs855641	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs860623	0.94[CEU][hapmap];0.83[CHB][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs863020	0.94[CEU][hapmap];0.83[CHB][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs941039	0.94[CEU][hapmap];0.83[CHB][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs941040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9941456	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9941467	0.87[CEU][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.80[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs855640	MAP3K10	cis	parietal	SCAN
rs855640	CCDC8	cis	parietal	SCAN
rs855640	SIPA1L3	cis	Heart Left Ventricle	GTEx
rs855640	BCAM	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38539200-38591200	Weak transcription	Small Intestine	intestine
2	chr19:38550800-38590000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr19:38551200-38613800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr19:38565600-38588400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr19:38567600-38605400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr19:38568000-38590200	Strong transcription	Fetal Intestine Small	intestine
7	chr19:38570800-38584000	Weak transcription	Right Atrium	heart
8	chr19:38570800-38590200	Weak transcription	Fetal Thymus	thymus
9	chr19:38571000-38580800	Weak transcription	Hela-S3	cervix
10	chr19:38571000-38590000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr19:38571000-38590200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr19:38571200-38590200	Weak transcription	HMEC	breast
13	chr19:38571200-38590200	Weak transcription	NHEK	skin
14	chr19:38571400-38586000	Strong transcription	A549	lung
15	chr19:38571800-38582600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr19:38571800-38585000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr19:38571800-38585400	Strong transcription	Fetal Stomach	stomach
18	chr19:38571800-38586000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr19:38571800-38586600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr19:38572000-38585800	Strong transcription	Primary B cells from peripheral blood	blood
21	chr19:38572000-38586000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr19:38572200-38585800	Weak transcription	NHDF-Ad	bronchial
23	chr19:38572400-38581400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr19:38573600-38586000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr19:38573600-38590000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr19:38573600-38610000	Strong transcription	Fetal Intestine Large	intestine
27	chr19:38573800-38584000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr19:38574000-38581000	Weak transcription	Brain Anterior Caudate	brain
29	chr19:38574000-38581000	Weak transcription	Brain Cingulate Gyrus	brain
30	chr19:38574000-38581000	Weak transcription	Left Ventricle	heart
31	chr19:38574000-38581200	Weak transcription	Brain Angular Gyrus	brain
32	chr19:38574000-38581200	Weak transcription	Pancreas	Pancrea
33	chr19:38574000-38584000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr19:38574000-38584000	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr19:38574000-38586000	Weak transcription	NHLF	lung
36	chr19:38574000-38590000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr19:38574000-38590200	Weak transcription	Aorta	Aorta
38	chr19:38574000-38590600	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr19:38574200-38589600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr19:38574200-38590200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr19:38574200-38590200	Weak transcription	HUVEC	blood vessel
42	chr19:38574400-38590000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr19:38575400-38586000	Weak transcription	Placenta	Placenta
44	chr19:38575600-38584600	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr19:38576200-38580600	Strong transcription	HSMM	muscle
46	chr19:38576400-38590000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr19:38577200-38582000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr19:38577200-38585000	Strong transcription	Primary B cells from cord blood	blood
49	chr19:38577200-38585600	Strong transcription	Duodenum Mucosa	Duodenum
50	chr19:38577400-38581800	Strong transcription	Rectal Mucosa Donor 31	rectum

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