Variant report

Variant	rs6482515
Chromosome Location	chr10:18827828-18827829
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	chr10:18824996..18829139-chr10:18831210..18835804,4	K562	blood:

Variant related genes	Relation type
ENSG00000240291	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10508562	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs10508563	0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs1055116	0.83[JPT][hapmap]
rs10741091	0.85[JPT][hapmap]
rs10741111	0.89[JPT][hapmap]
rs10741115	0.90[JPT][hapmap]
rs10764582	0.95[JPT][hapmap]
rs10764601	0.90[JPT][hapmap]
rs10764625	0.84[JPT][hapmap]
rs10828851	0.90[JPT][hapmap]
rs10828870	0.87[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs10828871	0.83[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs10828896	0.90[JPT][hapmap]
rs10828975	0.84[CHD][hapmap];0.90[JPT][hapmap]
rs10829022	0.90[JPT][hapmap]
rs10829058	0.89[JPT][hapmap]
rs10829070	0.90[JPT][hapmap]
rs11014981	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs11015312	0.90[JPT][hapmap]
rs11015435	0.94[CHB][hapmap]
rs11511084	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs11540309	0.80[CHD][hapmap];0.90[JPT][hapmap]
rs11815228	0.81[CHB][hapmap]
rs12762481	0.94[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap]
rs12764334	0.94[ASN][1000 genomes]
rs12764398	0.82[ASN][1000 genomes]
rs12766105	0.84[JPT][hapmap]
rs12766314	0.94[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap]
rs12767546	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12767923	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs12769425	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs12770851	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs12772009	0.82[CHB][hapmap]
rs12772522	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs12774593	0.88[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs12775446	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12778035	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs12781208	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs12784387	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs12784986	0.94[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap]
rs2130531	0.94[CHB][hapmap]
rs2171922	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs2228645	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2272274	0.87[CHD][hapmap];0.95[JPT][hapmap]
rs3740102	0.84[JPT][hapmap]
rs3740104	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs3817494	0.87[CHD][hapmap];0.90[JPT][hapmap]
rs4237349	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs4310518	0.87[CHB][hapmap];0.89[JPT][hapmap]
rs4314963	0.88[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs4445544	0.89[CHD][hapmap];0.90[JPT][hapmap]
rs4468242	0.94[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap]
rs4748481	0.88[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs4748482	0.83[ASN][1000 genomes]
rs4748488	0.84[CHD][hapmap];0.90[JPT][hapmap]
rs4748496	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs4748499	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs6482533	0.84[CHD][hapmap];0.89[JPT][hapmap]
rs6482597	0.90[JPT][hapmap]
rs7072624	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs7072963	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs7081461	0.84[JPT][hapmap]
rs7088091	0.90[JPT][hapmap]
rs7096923	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs7097001	0.80[ASN][1000 genomes]
rs7099260	0.82[CHD][hapmap];0.90[JPT][hapmap]
rs7099423	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs7100880	0.81[CHD][hapmap];0.90[JPT][hapmap]
rs7895784	0.87[CHD][hapmap];0.90[JPT][hapmap]
rs7897159	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs7898513	0.85[JPT][hapmap]
rs7904016	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs7904949	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs7905365	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs7917584	0.85[JPT][hapmap]
rs7922550	0.90[JPT][hapmap]
rs7922829	0.90[JPT][hapmap]
rs7923480	0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv550042	chr10:18683267-18994583	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer 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	16 gene(s)	inside rSNPs	diseases
2	nsv1042073	chr10:18806900-18838303	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	esv34545	chr10:18821185-18908294	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	esv1793653	chr10:18827828-18888369	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	esv1794817	chr10:18827828-18888369	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	esv1811259	chr10:18827828-18888369	ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	esv1840241	chr10:18827828-18888369	Enhancers Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	esv1841068	chr10:18827828-18888369	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	esv1851495	chr10:18827828-18888369	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6482515	RP11-499P20.2	cis	Thyroid	GTEx
rs6482515	ARL5B	Cis_1M	lymphoblastoid	RTeQTL
rs6482515	NSUN6	cis	lung	GTEx
rs6482515	FAM188A	cis	cerebellum	SCAN
rs6482515	CACNB2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18802600-18828000	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr10:18802600-18828200	Weak transcription	Lung	lung
3	chr10:18807400-18828000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr10:18808000-18828000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr10:18810400-18828000	Weak transcription	Brain Angular Gyrus	brain
6	chr10:18810600-18828200	Weak transcription	Aorta	Aorta
7	chr10:18810800-18828000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr10:18814000-18828000	Weak transcription	Esophagus	oesophagus
9	chr10:18815200-18843600	Weak transcription	A549	lung
10	chr10:18815800-18828000	Weak transcription	K562	blood
11	chr10:18816400-18830400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr10:18816400-18841800	Strong transcription	Liver	Liver
13	chr10:18816800-18829600	Weak transcription	HSMMtube	muscle
14	chr10:18817400-18829000	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr10:18818800-18828000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr10:18818800-18828400	Weak transcription	Fetal Thymus	thymus
17	chr10:18819600-18828000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr10:18819800-18829800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr10:18820000-18828400	Weak transcription	Fetal Muscle Leg	muscle
20	chr10:18820000-18829800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr10:18820800-18841600	Weak transcription	Hela-S3	cervix
22	chr10:18822000-18840400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr10:18822000-18848000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr10:18822200-18830400	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr10:18822400-18829600	Weak transcription	HSMM	muscle
26	chr10:18822400-18833600	Strong transcription	Primary T cells from cord blood	blood
27	chr10:18822600-18829000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr10:18822600-18830600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr10:18822800-18830600	Strong transcription	Left Ventricle	heart
30	chr10:18822800-18841800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr10:18823200-18831200	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr10:18823400-18830400	Strong transcription	Stomach Smooth Muscle	stomach
33	chr10:18823400-18830600	Strong transcription	Fetal Lung	lung
34	chr10:18823400-18834800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr10:18823600-18831000	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr10:18823600-18836600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr10:18823800-18830400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr10:18824000-18830600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr10:18824200-18829800	Weak transcription	Placenta	Placenta
40	chr10:18824200-18830600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr10:18824200-18831200	Strong transcription	Fetal Stomach	stomach
42	chr10:18824200-18831600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr10:18824200-18834800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr10:18824200-18846200	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr10:18824200-18850600	Weak transcription	NHLF	lung
46	chr10:18824400-18828200	Weak transcription	GM12878-XiMat	blood
47	chr10:18824400-18829600	Weak transcription	Fetal Kidney	kidney
48	chr10:18824800-18829600	Weak transcription	HepG2	liver
49	chr10:18825000-18830400	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr10:18825000-18835800	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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