Variant report

Variant	rs2133660
Chromosome Location	chr3:46031957-46031958
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	chr3:46023503..46025098-chr3:46030445..46033156,2	K562	blood:
2	chr3:45998846..46001598-chr3:46029585..46032027,2	K562	blood:

Variant related genes	Relation type
ENSG00000163820	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11130078	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11130082	0.92[CEU][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.94[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	0.93[ASW][hapmap];0.92[CEU][hapmap];0.89[GIH][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1392288	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[ASN][1000 genomes]
rs1463680	1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[ASN][1000 genomes]
rs1500003	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1846615	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1846616	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1873000	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1873001	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2129879	0.96[CEU][hapmap];0.83[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2129881	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2171528	0.96[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2171529	0.96[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2234350	0.88[ASN][1000 genomes]
rs2276855	0.96[ASN][1000 genomes]
rs2276856	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];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[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4683159	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.94[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	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7612402	0.96[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7628447	0.91[CEU][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7652331	0.80[GIH][hapmap]
rs9844821	1.00[ASN][1000 genomes]
rs9869848	0.88[ASN][1000 genomes]
rs9875616	1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[ASN][1000 genomes]

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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2133660	FYCO1	cis	lung	GTEx
rs2133660	CXCR6	cis	parietal	SCAN
rs2133660	NCKIPSD	cis	parietal	SCAN
rs2133660	CCR3	cis	Whole Blood	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46010200-46033000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:46013600-46034000	Genic enhancers	Fetal Thymus	thymus
3	chr3:46020000-46034200	Genic enhancers	Dnd41	blood
4	chr3:46021400-46036200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:46021600-46034000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:46025600-46032400	Enhancers	Stomach Mucosa	stomach
7	chr3:46025600-46033000	Enhancers	Right Ventricle	heart
8	chr3:46026200-46032000	Enhancers	Ovary	ovary
9	chr3:46026200-46032000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
10	chr3:46026200-46032000	Enhancers	NHLF	lung
11	chr3:46026400-46033800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr3:46026400-46034600	Genic enhancers	Primary T cells fromperipheralblood	blood
13	chr3:46026600-46032200	Enhancers	Liver	Liver
14	chr3:46026600-46032200	Enhancers	Duodenum Mucosa	Duodenum
15	chr3:46026600-46033000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr3:46026600-46033000	Weak transcription	Primary B cells from peripheral blood	blood
17	chr3:46026600-46033000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr3:46026600-46036200	Enhancers	Left Ventricle	heart
19	chr3:46026800-46032800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:46026800-46033400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:46026800-46033600	Weak transcription	Primary hematopoietic stem cells	blood
22	chr3:46026800-46033800	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr3:46026800-46035600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr3:46027000-46032200	Enhancers	Psoas Muscle	Psoas
25	chr3:46027200-46033400	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr3:46027200-46036000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:46027400-46032000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr3:46027400-46032000	Enhancers	HMEC	breast
29	chr3:46027400-46032800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr3:46027600-46033000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr3:46027600-46033400	Weak transcription	GM12878-XiMat	blood
32	chr3:46027600-46034400	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr3:46027800-46033800	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr3:46027800-46034000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr3:46028000-46034400	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr3:46028200-46034600	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr3:46028400-46035400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr3:46028600-46032000	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
39	chr3:46028800-46033000	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr3:46029400-46036200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr3:46029400-46036200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr3:46029400-46036200	Weak transcription	A549	lung
43	chr3:46029800-46032000	Enhancers	Brain Substantia Nigra	brain
44	chr3:46029800-46033000	Weak transcription	Primary T cells from cord blood	blood
45	chr3:46029800-46035800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr3:46029800-46036000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr3:46029800-46036000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:46030000-46032800	Weak transcription	Fetal Stomach	stomach
49	chr3:46030000-46033600	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr3:46030000-46033600	Weak transcription	HUES6 Cell Line	embryonic stem cell

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