Variant report

Variant	rs4859581
Chromosome Location	chr4:76906974-76906975
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	chr4:76902021..76904810-chr4:76904972..76908899,4	MCF-7	breast:
2	chr4:76906818..76908610-chr4:76910040..76912249,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198301	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10000130	0.80[ASN][1000 genomes]
rs10003240	0.80[ASN][1000 genomes]
rs10003382	0.80[ASN][1000 genomes]
rs10008757	0.92[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10014049	0.80[ASN][1000 genomes]
rs10014837	0.89[GIH][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.80[ASN][1000 genomes]
rs10017431	1.00[CHB][hapmap];0.86[GIH][hapmap];0.81[TSI][hapmap];0.80[ASN][1000 genomes]
rs10021768	0.86[GIH][hapmap];0.83[TSI][hapmap];0.80[ASN][1000 genomes]
rs10025102	0.80[ASN][1000 genomes]
rs10031452	0.84[ASW][hapmap];0.89[GIH][hapmap];0.86[LWK][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];0.91[YRI][hapmap];0.83[ASN][1000 genomes]
rs10336	0.92[ASW][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];0.83[LWK][hapmap];0.82[TSI][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs11097189	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11097212	0.86[GIH][hapmap];0.81[TSI][hapmap];0.80[ASN][1000 genomes]
rs11732759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11931349	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11947509	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13111710	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13125558	1.00[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs13126007	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13128319	0.86[GIH][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap]
rs13130018	0.80[ASN][1000 genomes]
rs13130221	0.80[ASN][1000 genomes]
rs13132564	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13138223	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1554013	0.83[ASN][1000 genomes]
rs2242471	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2242473	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2242474	1.00[ASW][hapmap];0.96[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];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2273	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292533	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28681066	0.86[ASN][1000 genomes]
rs4129781	0.80[ASN][1000 genomes]
rs4241578	0.80[ASN][1000 genomes]
rs4241579	0.80[ASN][1000 genomes]
rs4241580	0.80[ASN][1000 genomes]
rs4257674	0.80[ASN][1000 genomes]
rs4282209	0.92[CEU][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4302486	0.86[GIH][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.80[ASN][1000 genomes]
rs4304003	0.84[ASW][hapmap];0.84[GIH][hapmap]
rs4309862	0.80[ASN][1000 genomes]
rs4318674	0.83[ASN][1000 genomes]
rs4337760	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4356932	0.80[ASN][1000 genomes]
rs4371639	0.80[ASN][1000 genomes]
rs4380549	0.86[GIH][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap]
rs4386624	0.80[ASN][1000 genomes]
rs4417995	0.80[ASN][1000 genomes]
rs4422436	0.86[GIH][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap]
rs4456983	0.80[ASN][1000 genomes]
rs4478212	0.80[ASN][1000 genomes]
rs4512021	0.86[GIH][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap]
rs4580676	0.80[ASN][1000 genomes]
rs4583787	0.80[ASN][1000 genomes]
rs4616778	0.86[GIH][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap]
rs4619915	0.84[GIH][hapmap];0.81[TSI][hapmap];0.80[ASN][1000 genomes]
rs4859413	1.00[ASW][hapmap];0.96[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];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859414	0.89[GIH][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.80[ASN][1000 genomes]
rs4859415	0.86[GIH][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.80[ASN][1000 genomes]
rs4859582	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];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859584	0.89[GIH][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.80[ASN][1000 genomes]
rs4859586	0.80[ASN][1000 genomes]
rs4859587	0.80[ASN][1000 genomes]
rs4859588	0.89[GIH][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.80[ASN][1000 genomes]
rs4859591	0.80[ASN][1000 genomes]
rs4859594	0.83[ASN][1000 genomes]
rs4859595	0.80[ASN][1000 genomes]
rs4859597	0.80[ASN][1000 genomes]
rs4859598	0.80[ASN][1000 genomes]
rs4859600	0.80[ASN][1000 genomes]
rs6532078	0.96[CEU][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6532083	0.92[ASW][hapmap];0.82[CHB][hapmap];0.89[GIH][hapmap];0.86[LWK][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.91[YRI][hapmap];0.83[ASN][1000 genomes]
rs6532086	0.80[ASN][1000 genomes]
rs6532093	0.80[ASN][1000 genomes]
rs6532111	1.00[CHB][hapmap];0.86[GIH][hapmap];0.81[TSI][hapmap];0.80[ASN][1000 genomes]
rs6532114	0.86[GIH][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.80[ASN][1000 genomes]
rs6532121	0.84[ASW][hapmap];0.86[GIH][hapmap];0.80[MEX][hapmap]
rs6814012	0.80[ASN][1000 genomes]
rs6814817	0.80[ASN][1000 genomes]
rs6819597	0.86[GIH][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.80[ASN][1000 genomes]
rs6819920	0.80[ASN][1000 genomes]
rs6825045	0.80[ASN][1000 genomes]
rs6826085	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];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6828596	0.80[ASN][1000 genomes]
rs6844097	0.80[ASN][1000 genomes]
rs6845396	0.89[GIH][hapmap];0.83[TSI][hapmap];0.80[ASN][1000 genomes]
rs6850760	0.86[GIH][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.80[ASN][1000 genomes]
rs6852075	0.80[ASN][1000 genomes]
rs6856958	0.80[ASN][1000 genomes]
rs7436021	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7436646	0.86[GIH][hapmap];0.83[TSI][hapmap];0.80[ASN][1000 genomes]
rs7665152	0.80[ASN][1000 genomes]
rs7670789	0.80[ASN][1000 genomes]
rs7674409	0.86[GIH][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.80[ASN][1000 genomes]
rs7679177	0.83[EUR][1000 genomes]
rs7684461	0.86[GIH][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap]
rs8878	1.00[CHB][hapmap];0.89[GIH][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.80[ASN][1000 genomes]
rs9307050	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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9884374	0.80[ASN][1000 genomes]
rs9992952	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9995007	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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:20)

SNP	Gene	Cis/trans	Tissue	Source
rs4859581	NAAA	cis	lymphoblastoid	seeQTL
rs4859581	NAAA	cis	Muscle Skeletal	GTEx
rs4859581	NAAA	cis	Nerve Tibial	GTEx
rs4859581	NAAA	cis	Artery Aorta	GTEx
rs4859581	NAAA	cis	parietal	SCAN
rs4859581	ASAHL	cis	multi-tissue	Pritchard
rs4859581	CXCL11	cis	multi-tissue	Pritchard
rs4859581	ART3	cis	Nerve Tibial	GTEx
rs4859581	SLC6A20	trans	multi-tissue	Pritchard
rs4859581	CXCL10	cis	lymphoblastoid	seeQTL
rs4859581	NAAA	cis	Whole Blood	GTEx
rs4859581	NAAA	cis	cerebellum	SCAN
rs4859581	NAAA	cis	Skin Sun Exposed Lower leg	GTEx
rs4859581	NAAA	cis	Heart Left Ventricle	GTEx
rs4859581	NAAA	cis	Esophagus Mucosa	GTEx
rs4859581	NAAA	cis	lung	GTEx
rs4859581	NAAA	cis	Adipose Subcutaneous	GTEx
rs4859581	NAAA	cis	Lymphoblastoid	GTEx
rs4859581	NAAA	cis	Esophagus Muscularis	GTEx
rs4859581	NAAA	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76887200-76911000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr4:76887800-76909600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr4:76894200-76910200	Weak transcription	Small Intestine	intestine
4	chr4:76895400-76910400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr4:76895800-76910200	Weak transcription	Spleen	Spleen
6	chr4:76897600-76910000	Weak transcription	Stomach Mucosa	stomach
7	chr4:76898600-76909200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr4:76899200-76910200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr4:76899200-76910400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr4:76899400-76910400	Weak transcription	Fetal Lung	lung
11	chr4:76899800-76910000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr4:76900000-76907000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr4:76900000-76907200	Weak transcription	Psoas Muscle	Psoas
14	chr4:76900200-76911000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr4:76900400-76910200	Weak transcription	Ovary	ovary
16	chr4:76902000-76910400	Weak transcription	Brain Germinal Matrix	brain
17	chr4:76902000-76911000	Weak transcription	Aorta	Aorta
18	chr4:76902200-76908000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr4:76902200-76909000	Weak transcription	Colon Smooth Muscle	Colon
20	chr4:76902200-76909800	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr4:76902200-76910200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr4:76902200-76910800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:76902200-76911000	Weak transcription	Gastric	stomach
24	chr4:76902200-76911000	Weak transcription	Pancreas	Pancrea
25	chr4:76902200-76911200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr4:76902200-76911200	Weak transcription	Esophagus	oesophagus
27	chr4:76902400-76910200	Weak transcription	Colonic Mucosa	Colon
28	chr4:76902400-76910200	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr4:76902400-76910200	Weak transcription	HUVEC	blood vessel
30	chr4:76902400-76910600	Weak transcription	Fetal Kidney	kidney
31	chr4:76902600-76907200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr4:76902600-76907800	Weak transcription	Left Ventricle	heart
33	chr4:76902600-76908400	Weak transcription	Fetal Brain Female	brain
34	chr4:76902600-76909200	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr4:76902600-76909800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr4:76902600-76910000	Weak transcription	Thymus	Thymus
37	chr4:76902600-76910800	Weak transcription	Fetal Muscle Trunk	muscle
38	chr4:76902600-76911000	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr4:76902800-76909000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr4:76902800-76909200	Weak transcription	Adipose Nuclei	Adipose
41	chr4:76902800-76910000	Weak transcription	Brain Angular Gyrus	brain
42	chr4:76902800-76910200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr4:76902800-76910200	Weak transcription	Brain Substantia Nigra	brain
44	chr4:76902800-76910200	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr4:76902800-76910400	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr4:76902800-76910400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr4:76902800-76910600	Weak transcription	Fetal Brain Male	brain
48	chr4:76903000-76909000	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr4:76903000-76910000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr4:76903000-76910000	Weak transcription	Brain Anterior Caudate	brain

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