Variant report

Variant	rs2242470
Chromosome Location	chr4:76878688-76878689
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10007919	0.88[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap]
rs10009947	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10021434	0.84[CEU][hapmap];0.83[CHB][hapmap];0.88[JPT][hapmap];0.86[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10031733	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10031983	0.87[CEU][hapmap];0.81[CHB][hapmap]
rs10518143	0.94[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12374321	0.94[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12374370	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13111494	0.88[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap]
rs13112512	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13118503	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13129896	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13130917	0.88[CEU][hapmap];0.81[CHB][hapmap]
rs17001247	0.94[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1857821	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271528	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276886	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28375800	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28422144	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28451731	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28532601	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28535831	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28588114	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28595360	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28647886	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2869462	0.94[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34630680	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34740469	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3733238	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3796484	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4241577	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4859567	0.94[CEU][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs4859570	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4859571	0.94[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4859572	0.84[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4859573	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4859577	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859578	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859580	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859609	0.87[GIH][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap]
rs55876513	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66498356	0.90[ASN][1000 genomes]
rs6847815	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73825589	0.82[AFR][1000 genomes]
rs884004	0.94[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9994667	0.88[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3353539	chr4:76530136-76993859	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv529613	chr4:76654941-77081576	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv1004627	chr4:76793910-76999584	Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs2242470	NAAA	cis	Esophagus Mucosa	GTEx
rs2242470	CDKL2	cis	parietal	SCAN
rs2242470	ASAHL	cis	multi-tissue	Pritchard
rs2242470	NAAA	cis	parietal	SCAN
rs2242470	NAAA	cis	lymphoblastoid	seeQTL
rs2242470	RCHY1	cis	cerebellum	SCAN
rs2242470	CXCL10	cis	lymphoblastoid	seeQTL
rs2242470	NAAA	cis	cerebellum	SCAN
rs2242470	NAAA	cis	Whole Blood	GTEx
rs2242470	NAAA	cis	Artery Aorta	GTEx
rs2242470	FAM47E	cis	cerebellum	SCAN
rs2242470	NAAA	cis	Skin Sun Exposed Lower leg	GTEx
rs2242470	CXCL10	Cis_1M	lymphoblastoid	RTeQTL
rs2242470	NAAA	cis	Muscle Skeletal	GTEx
rs2242470	ASAHL	Cis_1M	lymphoblastoid	RTeQTL
rs2242470	NAAA	cis	Esophagus Muscularis	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76862000-76896600	Weak transcription	Stomach Mucosa	stomach
2	chr4:76862200-76886600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:76863000-76903600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr4:76863800-76884600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:76864600-76884800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr4:76864800-76883800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr4:76864800-76884400	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr4:76864800-76884600	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr4:76864800-76903000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr4:76866200-76883000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr4:76866400-76886800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr4:76866600-76883000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr4:76867400-76882600	Strong transcription	H1 Cell Line	embryonic stem cell
14	chr4:76867400-76882800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr4:76867400-76883000	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr4:76867400-76883200	Strong transcription	Osteobl	bone
17	chr4:76867400-76885600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr4:76867400-76886600	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr4:76867800-76882800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr4:76867800-76883000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr4:76867800-76883200	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr4:76867800-76883400	Strong transcription	Fetal Muscle Trunk	muscle
23	chr4:76867800-76884600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr4:76867800-76888800	Strong transcription	Liver	Liver
25	chr4:76867800-76900000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr4:76867800-76903800	Strong transcription	Fetal Thymus	thymus
27	chr4:76868000-76882800	Strong transcription	Adipose Nuclei	Adipose
28	chr4:76868000-76882800	Strong transcription	Left Ventricle	heart
29	chr4:76868000-76883000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr4:76868000-76884600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr4:76868000-76884800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr4:76868000-76886400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr4:76868000-76886600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr4:76868000-76899800	Strong transcription	Skeletal Muscle Male	skeletal muscle
35	chr4:76868000-76903000	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr4:76868000-76903000	Strong transcription	Stomach Smooth Muscle	stomach
37	chr4:76868000-76903800	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr4:76868200-76882800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr4:76868200-76903400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr4:76868200-76903600	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr4:76868400-76882800	Strong transcription	Dnd41	blood
42	chr4:76868400-76903600	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr4:76868400-76903800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr4:76868400-76903800	Strong transcription	Placenta	Placenta
45	chr4:76869200-76900200	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr4:76869800-76882800	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr4:76870000-76886800	Strong transcription	Primary T cells from cord blood	blood
48	chr4:76870600-76882800	Strong transcription	Fetal Intestine Large	intestine
49	chr4:76870600-76883000	Strong transcription	Duodenum Mucosa	Duodenum
50	chr4:76870800-76882800	Strong transcription	Fetal Brain Female	brain

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