Variant report

Variant	rs2682586
Chromosome Location	chr19:44081499-44081500
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:44077678..44083171-chr19:44093489..44103015,14	K562	blood:
2	chr19:44078955..44081902-chr19:44082644..44085623,4	MCF-7	breast:
3	chr19:44079733..44081896-chr19:44082367..44084669,4	K562	blood:
4	chr19:44077687..44082496-chr19:44098234..44103069,7	MCF-7	breast:
5	chr19:44077515..44081647-chr19:44122454..44125105,4	K562	blood:
6	chr19:43991164..43993354-chr19:44079151..44081521,2	K562	blood:
7	chr19:44079920..44081896-chr19:44082367..44084716,3	K562	blood:

Variant related genes	Relation type
ENSG00000268361	Chromatin interaction
ENSG00000073050	Chromatin interaction
ENSG00000226763	Chromatin interaction
ENSG00000124444	Chromatin interaction
ENSG00000176531	Chromatin interaction
ENSG00000234465	Chromatin interaction
ENSG00000167378	Chromatin interaction
ENSG00000131116	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10402946	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs12973764	0.89[CEU][hapmap];0.86[MEX][hapmap]
rs12980646	0.94[CEU][hapmap];0.86[MEX][hapmap]
rs12981023	0.88[CEU][hapmap]
rs17655646	1.00[CHB][hapmap]
rs184239	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1978008	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2030404	0.86[CHD][hapmap];0.89[JPT][hapmap]
rs2102954	0.89[CEU][hapmap]
rs2599462	0.86[CHD][hapmap];0.89[JPT][hapmap]
rs2682563	0.86[CHD][hapmap];0.89[JPT][hapmap]
rs2682585	0.83[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2854501	0.91[ASW][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2854506	1.00[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2854507	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2854508	1.00[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2854509	0.92[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs304731	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3213255	0.81[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3213263	0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3213276	0.88[ASN][1000 genomes]
rs3213295	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3213334	0.92[ASW][hapmap];0.84[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.84[MKK][hapmap];0.88[TSI][hapmap];0.92[YRI][hapmap]
rs3213356	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs4802183	0.89[CEU][hapmap]
rs4802185	0.89[CEU][hapmap];0.86[MEX][hapmap]
rs4803646	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs7251275	1.00[CHB][hapmap]
rs7253856	0.83[CEU][hapmap];0.86[MEX][hapmap]
rs762506	1.00[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs762507	0.86[CHD][hapmap];1.00[JPT][hapmap]

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	nsv1056721	chr19:43808474-44095077	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
3	nsv1056785	chr19:44010370-44081601	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv1063149	chr19:44059081-44087583	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2682586	GPR4	cis	parietal	SCAN
rs2682586	ETHE1	cis	lymphoblastoid	seeQTL
rs2682586	XRCC1	cis	lymphoblastoid	seeQTL
rs2682586	BLOC1S3	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44079200-44081600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr19:44079800-44084000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr19:44079800-44085400	Weak transcription	Gastric	stomach
4	chr19:44079800-44098200	Weak transcription	Small Intestine	intestine
5	chr19:44080200-44084000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:44080400-44081600	Enhancers	HMEC	breast
7	chr19:44080400-44082400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr19:44080400-44083800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr19:44080400-44084000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr19:44080400-44084000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr19:44080400-44084000	Weak transcription	Brain Angular Gyrus	brain
12	chr19:44080400-44084000	Weak transcription	Brain Anterior Caudate	brain
13	chr19:44080400-44084000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr19:44080400-44084000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr19:44080400-44084000	Weak transcription	NHLF	lung
16	chr19:44080400-44084200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr19:44080400-44084200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr19:44080400-44084200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr19:44080400-44084200	Weak transcription	Liver	Liver
20	chr19:44080400-44084200	Weak transcription	Left Ventricle	heart
21	chr19:44080400-44084200	Weak transcription	Lung	lung
22	chr19:44080400-44084200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr19:44080400-44084200	Weak transcription	Right Atrium	heart
24	chr19:44080400-44084200	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr19:44080400-44084200	Weak transcription	HUVEC	blood vessel
26	chr19:44080400-44090200	Weak transcription	HSMM	muscle
27	chr19:44080600-44083800	Weak transcription	Primary hematopoietic stem cells	blood
28	chr19:44080600-44083800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr19:44080600-44083800	Weak transcription	Fetal Lung	lung
30	chr19:44080600-44084000	Weak transcription	Primary T cells from cord blood	blood
31	chr19:44080600-44084000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr19:44080600-44084000	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr19:44080600-44084000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr19:44080600-44084000	Weak transcription	Brain Hippocampus Middle	brain
35	chr19:44080600-44084000	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr19:44080600-44084000	Weak transcription	Brain Substantia Nigra	brain
37	chr19:44080600-44084000	Weak transcription	Colonic Mucosa	Colon
38	chr19:44080600-44084000	Weak transcription	Colon Smooth Muscle	Colon
39	chr19:44080600-44084000	Weak transcription	Fetal Intestine Large	intestine
40	chr19:44080600-44084000	Weak transcription	Fetal Intestine Small	intestine
41	chr19:44080600-44084000	Weak transcription	Ovary	ovary
42	chr19:44080600-44084000	Weak transcription	Rectal Smooth Muscle	rectum
43	chr19:44080600-44084000	Weak transcription	K562	blood
44	chr19:44080600-44084000	Weak transcription	NH-A	brain
45	chr19:44080600-44084200	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr19:44080600-44084200	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr19:44080600-44084200	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr19:44080600-44084200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr19:44080600-44084200	Weak transcription	Right Ventricle	heart
50	chr19:44080600-44084400	Weak transcription	Spleen	Spleen

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