Variant report

Variant	rs1554015
Chromosome Location	chr4:76889094-76889095
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	chr4:76879502..76881277-chr4:76887911..76890255,2	K562	blood:
2	chr4:76886922..76890200-chr4:76895899..76900311,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198301	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10019066	0.85[JPT][hapmap]
rs10222911	0.94[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1050176	0.95[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10856871	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11097192	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12499668	0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap]
rs12500200	0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12504339	0.83[LWK][hapmap];0.86[YRI][hapmap]
rs12504915	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs12509996	0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap]
rs12511352	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs12511357	0.85[CHB][hapmap]
rs12511359	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs12511861	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13106039	0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap]
rs17001275	0.91[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17001284	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1910907	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2869461	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.95[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28703679	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3733236	0.82[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4621456	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs4859412	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55964684	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56039229	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56105413	0.98[EUR][1000 genomes]
rs56316945	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58909712	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59559903	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61279846	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6532084	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6532167	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs6532168	0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap]
rs6532169	0.85[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap]
rs6532170	0.85[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap]
rs66477189	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67210456	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67297326	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67413521	0.85[ASN][1000 genomes]
rs67687266	0.88[ASN][1000 genomes]
rs6828744	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6834291	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];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6847716	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6857358	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72651379	0.90[EUR][1000 genomes]
rs72651387	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7349626	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7666094	1.00[GIH][hapmap];0.84[JPT][hapmap]
rs7670156	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7671125	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7679689	0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap]
rs7685390	0.85[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap]
rs7692605	0.82[CHB][hapmap]
rs7693606	0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap]
rs7696286	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9998233	0.85[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1554015	NAAA	cis	lymphoblastoid	seeQTL

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	chr4:76863000-76903600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr4:76864800-76903000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr4:76867800-76900000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr4:76867800-76903800	Strong transcription	Fetal Thymus	thymus
6	chr4:76868000-76899800	Strong transcription	Skeletal Muscle Male	skeletal muscle
7	chr4:76868000-76903000	Strong transcription	Skeletal Muscle Female	skeletal muscle
8	chr4:76868000-76903000	Strong transcription	Stomach Smooth Muscle	stomach
9	chr4:76868000-76903800	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr4:76868200-76903400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr4:76868200-76903600	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr4:76868400-76903600	Strong transcription	Primary T helper cells PMA-I stimulated	--
13	chr4:76868400-76903800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr4:76868400-76903800	Strong transcription	Placenta	Placenta
15	chr4:76869200-76900200	Strong transcription	Duodenum Smooth Muscle	Duodenum
16	chr4:76870800-76897600	Strong transcription	Brain Germinal Matrix	brain
17	chr4:76872200-76902800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr4:76876800-76895200	Strong transcription	Fetal Kidney	kidney
19	chr4:76880600-76893400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr4:76882400-76898200	Weak transcription	Aorta	Aorta
21	chr4:76883800-76899800	Strong transcription	Muscle Satellite Cultured Cells	--
22	chr4:76883800-76903000	Strong transcription	Duodenum Mucosa	Duodenum
23	chr4:76884000-76902800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr4:76884200-76899600	Strong transcription	Placenta Amnion	Placenta Amnion
25	chr4:76884200-76899800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr4:76884200-76902800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr4:76884200-76903800	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr4:76884400-76893000	Strong transcription	Brain Anterior Caudate	brain
29	chr4:76884400-76897400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr4:76884600-76889400	Strong transcription	Ovary	ovary
31	chr4:76884600-76889800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
32	chr4:76884600-76893400	Strong transcription	HSMMtube	muscle
33	chr4:76884600-76895600	Strong transcription	Fetal Brain Female	brain
34	chr4:76884600-76895800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
35	chr4:76884600-76896000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr4:76884600-76897400	Strong transcription	Brain Inferior Temporal Lobe	brain
37	chr4:76884600-76899800	Strong transcription	NH-A	brain
38	chr4:76884600-76899800	Strong transcription	Osteobl	bone
39	chr4:76884600-76902800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr4:76884600-76902800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr4:76884600-76902800	Strong transcription	Adipose Nuclei	Adipose
42	chr4:76884600-76903400	Strong transcription	HMEC	breast
43	chr4:76884600-76903400	Strong transcription	HSMM	muscle
44	chr4:76884600-76903600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr4:76884600-76903600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr4:76884600-76903800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr4:76884800-76892400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr4:76884800-76893600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
49	chr4:76884800-76893600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr4:76884800-76895400	Strong transcription	Brain Angular Gyrus	brain

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