Variant report

Variant	rs863020
Chromosome Location	chr19:38612993-38612994
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38611783..38614608-chr19:38870393..38872975,2	K562	blood:

Variant related genes	Relation type
ENSG00000099341	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10403716	0.85[EUR][1000 genomes]
rs10405667	0.88[EUR][1000 genomes]
rs10412762	0.94[CEU][hapmap];0.90[CHB][hapmap]
rs10420506	0.80[CEU][hapmap];0.90[CHB][hapmap]
rs10422665	0.93[CEU][hapmap];0.90[JPT][hapmap]
rs1568975	0.88[EUR][1000 genomes]
rs1614979	0.94[CEU][hapmap];0.83[CHB][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs1622409	0.89[EUR][1000 genomes]
rs1625884	0.91[EUR][1000 genomes]
rs1654355	0.88[EUR][1000 genomes]
rs1654357	0.89[EUR][1000 genomes]
rs1654358	0.89[EUR][1000 genomes]
rs1654359	0.89[EUR][1000 genomes]
rs1654365	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs1654367	0.88[EUR][1000 genomes]
rs1725461	0.87[EUR][1000 genomes]
rs1725473	0.90[EUR][1000 genomes]
rs1725479	0.89[EUR][1000 genomes]
rs1725512	0.94[CEU][hapmap];0.83[CHB][hapmap];0.84[EUR][1000 genomes]
rs2005054	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2082442	0.91[EUR][1000 genomes]
rs2082443	0.91[EUR][1000 genomes]
rs28581256	0.95[EUR][1000 genomes]
rs3760882	0.91[EUR][1000 genomes]
rs3810356	0.91[EUR][1000 genomes]
rs4802233	0.94[CEU][hapmap];0.83[CHB][hapmap];0.89[EUR][1000 genomes]
rs4802239	0.91[EUR][1000 genomes]
rs4802247	0.95[EUR][1000 genomes]
rs4802256	0.94[CEU][hapmap];0.90[CHB][hapmap]
rs4802278	0.81[CHB][hapmap]
rs4803786	0.97[EUR][1000 genomes]
rs4803800	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4803801	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4803802	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4803803	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4803809	0.91[EUR][1000 genomes]
rs4803810	0.91[EUR][1000 genomes]
rs4803828	0.80[CEU][hapmap];0.90[CHB][hapmap]
rs4803829	0.80[CEU][hapmap];0.90[CHB][hapmap]
rs4803862	0.81[CHB][hapmap]
rs56166457	0.92[EUR][1000 genomes]
rs56293547	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs58152231	0.89[EUR][1000 genomes]
rs59185302	0.97[EUR][1000 genomes]
rs59579475	0.92[EUR][1000 genomes]
rs59924887	0.97[EUR][1000 genomes]
rs61388128	0.97[EUR][1000 genomes]
rs705505	0.89[EUR][1000 genomes]
rs71179415	0.90[EUR][1000 genomes]
rs7248428	0.86[EUR][1000 genomes]
rs7250034	0.91[EUR][1000 genomes]
rs729625	0.88[EUR][1000 genomes]
rs729626	0.89[EUR][1000 genomes]
rs735615	0.89[EUR][1000 genomes]
rs754123	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8105468	0.97[EUR][1000 genomes]
rs8106266	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs855603	0.94[CEU][hapmap]
rs855619	0.89[EUR][1000 genomes]
rs855621	0.89[EUR][1000 genomes]
rs855623	0.89[EUR][1000 genomes]
rs855624	0.89[EUR][1000 genomes]
rs855625	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs855627	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs855630	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs855631	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs855633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs855634	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs855638	0.89[EUR][1000 genomes]
rs855640	0.89[EUR][1000 genomes]
rs855641	0.91[EUR][1000 genomes]
rs860623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs941039	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs941040	0.94[CEU][hapmap];0.83[CHB][hapmap];0.89[EUR][1000 genomes]
rs9941456	0.91[EUR][1000 genomes]
rs9941467	0.94[CEU][hapmap];0.90[CHB][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	esv1804371	chr19:38610640-38616928	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs863020	BCAM	cis	parietal	SCAN
rs863020	CCDC8	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38551200-38613800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr19:38587200-38613600	Strong transcription	Cortex derived primary cultured neurospheres	brain
3	chr19:38587400-38613400	Strong transcription	Duodenum Mucosa	Duodenum
4	chr19:38591800-38642800	Weak transcription	Small Intestine	intestine
5	chr19:38596000-38613800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr19:38600600-38652800	Weak transcription	NHDF-Ad	bronchial
7	chr19:38603000-38625400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr19:38604000-38613400	Strong transcription	Primary B cells from cord blood	blood
9	chr19:38605800-38625400	Weak transcription	HMEC	breast
10	chr19:38606000-38613000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr19:38606200-38613800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr19:38607200-38613800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr19:38607600-38613200	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr19:38607600-38613400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr19:38607600-38613800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr19:38607600-38613800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr19:38607800-38613800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr19:38608400-38613800	Strong transcription	Liver	Liver
19	chr19:38608800-38613600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr19:38608800-38614000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr19:38608800-38614000	ZNF genes & repeats	Fetal Intestine Small	intestine
22	chr19:38609400-38613000	Strong transcription	Brain Germinal Matrix	brain
23	chr19:38609400-38613800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr19:38609600-38613800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr19:38609800-38613400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr19:38610000-38613400	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr19:38610000-38613400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr19:38610000-38613800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr19:38610400-38613000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr19:38610400-38613000	Weak transcription	Colonic Mucosa	Colon
31	chr19:38610600-38613000	Weak transcription	Pancreas	Pancrea
32	chr19:38610600-38613200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr19:38610600-38613400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr19:38610600-38613800	Strong transcription	Ovary	ovary
35	chr19:38610800-38643600	Weak transcription	HepG2	liver
36	chr19:38611000-38613000	Weak transcription	Spleen	Spleen
37	chr19:38611000-38613000	Weak transcription	NHLF	lung
38	chr19:38611000-38652800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr19:38611200-38625400	Weak transcription	NHEK	skin
40	chr19:38611400-38613000	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr19:38611400-38613000	Weak transcription	K562	blood
42	chr19:38611600-38613000	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr19:38611600-38613000	Weak transcription	Brain Angular Gyrus	brain
44	chr19:38611600-38613000	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr19:38611600-38613000	Weak transcription	Brain Substantia Nigra	brain
46	chr19:38611600-38613000	Weak transcription	Fetal Muscle Trunk	muscle
47	chr19:38611600-38613000	Weak transcription	Left Ventricle	heart
48	chr19:38611600-38613000	Weak transcription	Lung	lung
49	chr19:38611600-38613000	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr19:38611600-38613000	Weak transcription	Dnd41	blood

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