Variant report

Variant	rs1500003
Chromosome Location	chr3:46033819-46033820
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:45985845..45987639-chr3:46033798..46035910,2	K562	blood:
2	chr3:46026501..46029475-chr3:46032165..46035137,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-XCR1-2	chr3:46033520-46037161	ucscGeneNc_uc003cpd_1

Variant related genes	Relation type
ENSG00000172215	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11130078	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11130082	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12053895	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12485445	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13064616	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13084541	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13086858	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1392288	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1463680	0.88[ASN][1000 genomes]
rs1846615	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1846616	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1873000	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1873001	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2129879	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2129881	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2133660	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2171528	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2171529	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2234350	0.88[ASN][1000 genomes]
rs2276855	0.96[ASN][1000 genomes]
rs2276856	0.82[ASN][1000 genomes]
rs2373089	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2373090	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35283688	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3796374	1.00[ASN][1000 genomes]
rs3947589	1.00[ASN][1000 genomes]
rs4683159	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4683165	0.91[ASN][1000 genomes]
rs55844314	1.00[ASN][1000 genomes]
rs57542549	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57651127	0.96[ASN][1000 genomes]
rs57837898	0.96[ASN][1000 genomes]
rs751667	0.96[ASN][1000 genomes]
rs7612402	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7628447	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9844821	1.00[ASN][1000 genomes]
rs9869848	0.88[ASN][1000 genomes]
rs9875616	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv2756987	chr3:46016464-46120400	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	esv2759145	chr3:46016464-46120400	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	esv1805205	chr3:46032847-46111081	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1500003	CCR3	cis	Whole Blood	GTEx
rs1500003	FYCO1	cis	lung	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46013600-46034000	Genic enhancers	Fetal Thymus	thymus
2	chr3:46020000-46034200	Genic enhancers	Dnd41	blood
3	chr3:46021400-46036200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:46021600-46034000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:46026400-46034600	Genic enhancers	Primary T cells fromperipheralblood	blood
6	chr3:46026600-46036200	Enhancers	Left Ventricle	heart
7	chr3:46026800-46035600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:46027200-46036000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:46027600-46034400	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr3:46027800-46034000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr3:46028000-46034400	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr3:46028200-46034600	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr3:46028400-46035400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr3:46029400-46036200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr3:46029400-46036200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:46029400-46036200	Weak transcription	A549	lung
17	chr3:46029800-46035800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:46029800-46036000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr3:46029800-46036000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:46030000-46034000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr3:46030000-46034400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:46030000-46034600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:46030000-46034600	Enhancers	Colon Smooth Muscle	Colon
24	chr3:46030000-46036000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr3:46030000-46036000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr3:46030200-46035000	Weak transcription	Fetal Lung	lung
27	chr3:46030200-46036200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr3:46030600-46036000	Weak transcription	Fetal Intestine Small	intestine
29	chr3:46030800-46034400	Weak transcription	Placenta	Placenta
30	chr3:46030800-46036000	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr3:46030800-46036200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr3:46031000-46035400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr3:46031200-46034800	Weak transcription	HepG2	liver
34	chr3:46031400-46034400	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr3:46031400-46035800	Weak transcription	Brain Germinal Matrix	brain
36	chr3:46031400-46035800	Weak transcription	Hela-S3	cervix
37	chr3:46031400-46036200	Weak transcription	HUVEC	blood vessel
38	chr3:46031600-46034000	Genic enhancers	Thymus	Thymus
39	chr3:46031800-46035800	Weak transcription	NHEK	skin
40	chr3:46031800-46036000	Weak transcription	Brain Angular Gyrus	brain
41	chr3:46031800-46036200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr3:46031800-46036200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr3:46031800-46036200	Weak transcription	Brain Cingulate Gyrus	brain
44	chr3:46032000-46034400	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr3:46032000-46036000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr3:46032000-46036200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr3:46032000-46036200	Weak transcription	HMEC	breast
48	chr3:46032200-46036200	Enhancers	Fetal Heart	heart
49	chr3:46032200-46036200	Weak transcription	Fetal Intestine Large	intestine
50	chr3:46032600-46035600	Enhancers	Liver	Liver

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