Variant report

Variant	rs4802256
Chromosome Location	chr19:38654551-38654552
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10401165	0.89[ASN][1000 genomes]
rs10403716	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10412762	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10412865	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10413751	0.81[JPT][hapmap]
rs10420506	0.87[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10422665	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1614979	0.87[CEU][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap]
rs1654349	0.81[JPT][hapmap]
rs1654365	0.87[CEU][hapmap];0.90[CHB][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap]
rs1725475	0.81[JPT][hapmap]
rs1725512	0.87[CEU][hapmap];0.81[JPT][hapmap]
rs2005054	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2010234	0.86[YRI][hapmap]
rs2082442	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2082443	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28495744	0.85[ASN][1000 genomes]
rs28581256	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4802233	0.87[CEU][hapmap];0.81[JPT][hapmap]
rs4802247	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4802278	0.81[CEU][hapmap];0.90[CHB][hapmap];0.90[TSI][hapmap]
rs4803786	0.93[ASN][1000 genomes]
rs4803800	0.82[EUR][1000 genomes]
rs4803801	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4803802	0.82[EUR][1000 genomes]
rs4803803	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4803809	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803810	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803828	0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4803829	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4803862	0.81[CEU][hapmap];0.90[CHB][hapmap];0.90[TSI][hapmap]
rs56166457	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59185302	0.93[ASN][1000 genomes]
rs59579475	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59924887	0.93[ASN][1000 genomes]
rs61388128	0.93[ASN][1000 genomes]
rs6508767	0.89[ASN][1000 genomes]
rs71179415	0.82[ASN][1000 genomes]
rs7245788	0.93[ASN][1000 genomes]
rs7248428	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7250034	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7256332	0.85[ASN][1000 genomes]
rs73627654	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73627663	0.93[ASN][1000 genomes]
rs73627676	0.93[ASN][1000 genomes]
rs73627686	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73930553	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs754123	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8105468	0.93[ASN][1000 genomes]
rs855601	0.81[JPT][hapmap]
rs855603	0.87[CEU][hapmap];0.81[JPT][hapmap]
rs855633	0.94[CEU][hapmap];0.90[CHB][hapmap]
rs855636	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs855637	0.81[JPT][hapmap]
rs860623	0.94[CEU][hapmap];0.90[CHB][hapmap];0.83[MEX][hapmap]
rs863020	0.94[CEU][hapmap];0.90[CHB][hapmap]
rs941039	0.94[CEU][hapmap];0.90[CHB][hapmap]
rs941040	0.87[CEU][hapmap];0.81[JPT][hapmap]
rs9941456	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9941467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][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	nsv833821	chr19:38629937-38756792	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4802256	BCAM	cis	parietal	SCAN
rs4802256	CCDC8	cis	parietal	SCAN
rs4802256	FCGBP	cis	parietal	SCAN
rs4802256	SIPA1L3	cis	Heart Left Ventricle	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38638200-38667200	Strong transcription	Cortex derived primary cultured neurospheres	brain
2	chr19:38643800-38654800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr19:38644000-38659200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr19:38645600-38660800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr19:38646000-38661000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr19:38651400-38658400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr19:38652400-38656400	Strong transcription	HepG2	liver
8	chr19:38652400-38657400	Strong transcription	Brain Angular Gyrus	brain
9	chr19:38652600-38655800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr19:38652600-38656400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
11	chr19:38653000-38655400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr19:38653200-38654600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr19:38653400-38656400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr19:38653400-38657800	Strong transcription	Colonic Mucosa	Colon
15	chr19:38653400-38658400	Strong transcription	Rectal Smooth Muscle	rectum
16	chr19:38653400-38658800	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr19:38653400-38659600	Strong transcription	Primary B cells from cord blood	blood
18	chr19:38653400-38659600	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr19:38653400-38660400	Strong transcription	GM12878-XiMat	blood
20	chr19:38653400-38661400	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr19:38653400-38663400	Strong transcription	Sigmoid Colon	Sigmoid Colon
22	chr19:38653600-38655000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr19:38653600-38655000	Weak transcription	Stomach Mucosa	stomach
24	chr19:38653600-38656200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr19:38653600-38656200	Strong transcription	Brain Anterior Caudate	brain
26	chr19:38653600-38656200	Strong transcription	Brain Cingulate Gyrus	brain
27	chr19:38653600-38656200	Strong transcription	Brain Inferior Temporal Lobe	brain
28	chr19:38653600-38656200	Strong transcription	HSMM	muscle
29	chr19:38653600-38656200	Strong transcription	HSMMtube	muscle
30	chr19:38653600-38656400	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr19:38653600-38656400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr19:38653600-38656400	Strong transcription	Pancreatic Islets	Pancreatic Islet
33	chr19:38653600-38656400	Strong transcription	Right Ventricle	heart
34	chr19:38653600-38657400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr19:38653600-38657600	Strong transcription	H1 Cell Line	embryonic stem cell
36	chr19:38653600-38657600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr19:38653600-38657600	Strong transcription	Left Ventricle	heart
38	chr19:38653600-38657600	Strong transcription	NH-A	brain
39	chr19:38653600-38658400	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr19:38653600-38658600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr19:38653600-38658600	Strong transcription	Ovary	ovary
42	chr19:38653600-38659000	Weak transcription	Fetal Heart	heart
43	chr19:38653600-38659200	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr19:38653600-38659600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr19:38653600-38659800	Weak transcription	Fetal Brain Male	brain
46	chr19:38653600-38660200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr19:38653600-38660200	Strong transcription	Primary T cells from cord blood	blood
48	chr19:38653600-38660400	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr19:38653600-38661200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr19:38653600-38661200	Strong transcription	Duodenum Mucosa	Duodenum

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