Variant report

Variant	rs13096474
Chromosome Location	chr3:49443081-49443082
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49441534..49443566-chr3:49445020..49447765,2	K562	blood:
2	chr3:49441705..49446563-chr3:49447849..49450189,5	MCF-7	breast:
3	chr3:49443013..49445153-chr3:49447014..49449649,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000067560	Chromatin interaction
ENSG00000145022	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 39 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs1009051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10154992	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs10155014	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865956	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs1106620	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11130186	0.91[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap]
rs11130187	0.81[AMR][1000 genomes]
rs11130190	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11130208	1.00[CHD][hapmap];0.83[LWK][hapmap];0.92[MKK][hapmap]
rs11710434	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11715060	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11719762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720542	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11720657	0.86[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11923032	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs11928090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12583	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs13322887	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs1464569	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1491983	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[LWK][hapmap];0.92[MKK][hapmap]
rs17080510	1.00[CHB][hapmap]
rs1982861	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140270	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2177268	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2312462	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329025	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3448	1.00[CEU][hapmap];1.00[GIH][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34890793	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap]
rs3866330	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3870339	0.95[CEU][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3870341	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3905330	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4052546	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4241405	1.00[CHD][hapmap];0.89[MKK][hapmap]
rs4241407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855853	0.80[EUR][1000 genomes]
rs4855858	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855869	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4955413	0.88[EUR][1000 genomes]
rs4955417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs4955424	0.89[EUR][1000 genomes]
rs4955425	0.89[EUR][1000 genomes]
rs4955430	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4955439	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap]
rs4955443	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap]
rs56127630	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs57273516	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62259933	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62259943	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62259944	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62259947	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62261183	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62261249	0.82[EUR][1000 genomes]
rs6446257	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap]
rs6446262	0.92[EUR][1000 genomes]
rs6446275	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6446285	1.00[CHD][hapmap]
rs6769744	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6769821	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap]
rs6775069	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs6778080	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap]
rs6783003	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs6784203	0.89[EUR][1000 genomes]
rs6785045	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6790105	0.83[EUR][1000 genomes]
rs6796147	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6805609	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6809204	0.87[EUR][1000 genomes]
rs6809851	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap]
rs72934271	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73088137	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7355800	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7374731	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7613491	0.88[EUR][1000 genomes]
rs7619016	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap]
rs7619789	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7620024	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7622786	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7625857	0.81[EUR][1000 genomes]
rs7626076	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap]
rs7638750	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7644148	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs7647973	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7648995	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7651372	0.85[EUR][1000 genomes]
rs7653505	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs8897	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs940045	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][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];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9654010	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs974495	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][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];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9757181	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9809237	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9812360	0.85[EUR][1000 genomes]
rs9817807	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9842132	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9847585	0.80[EUR][1000 genomes]
rs9860055	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9860285	0.84[EUR][1000 genomes]
rs9861027	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9862534	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9871024	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs9881860	1.00[CEU][hapmap];0.82[EUR][1000 genomes]

mRNA abundance (count:39)

SNP	Gene	Cis/trans	Tissue	Source
rs13096474	AMT	cis	Esophagus Muscularis	GTEx
rs13096474	WDR6	cis	Nerve Tibial	GTEx
rs13096474	WDR6	cis	Muscle Skeletal	GTEx
rs13096474	AMT	cis	Adipose Subcutaneous	GTEx
rs13096474	AMT	cis	parietal	SCAN
rs13096474	LZTFL1	cis	cerebellum	SCAN
rs13096474	NME6	cis	cerebellum	SCAN
rs13096474	GPX1	cis	parietal	SCAN
rs13096474	AMT	cis	lung	GTEx
rs13096474	AMT	cis	Thyroid	GTEx
rs13096474	AMT	cis	Artery Aorta	GTEx
rs13096474	ZNF589	cis	parietal	SCAN
rs13096474	GMPPB	cis	parietal	SCAN
rs13096474	AMT	cis	Nerve Tibial	GTEx
rs13096474	WDR6	cis	parietal	SCAN
rs13096474	SEMA3G	cis	cerebellum	SCAN
rs13096474	AMT	cis	Esophagus Mucosa	GTEx
rs13096474	AMT	cis	Skin Sun Exposed Lower leg	GTEx
rs13096474	NCKIPSD	cis	multi-tissue	Pritchard
rs13096474	WDR6	cis	multi-tissue	Pritchard
rs13096474	WDR6	cis	lung	GTEx
rs13096474	P4HTM	cis	parietal	SCAN
rs13096474	AMT	cis	cerebellum	SCAN
rs13096474	NICN1	cis	cerebellum	SCAN
rs13096474	WDR6	cis	Esophagus Muscularis	GTEx
rs13096474	DALRD3	cis	cerebellum	SCAN
rs13096474	AMT	cis	Muscle Skeletal	GTEx
rs13096474	AMT	cis	multi-tissue	Pritchard
rs13096474	QRICH1	cis	cerebellum	SCAN
rs13096474	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs13096474	DALRD3	cis	parietal	SCAN
rs13096474	AMT	cis	Artery Tibial	GTEx
rs13096474	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs13096474	RNF123	cis	parietal	SCAN
rs13096474	NICN1-AS1	cis	Thyroid	GTEx
rs13096474	NICN1	cis	multi-tissue	Pritchard
rs13096474	WDR6	cis	cerebellum	SCAN
rs13096474	NICN1	cis	Thyroid	GTEx
rs13096474	AMT	cis	Whole Blood	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49399000-49448000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:49406000-49445200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:49413200-49447400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:49424200-49443400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:49426000-49444000	Weak transcription	Esophagus	oesophagus
6	chr3:49427000-49448400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:49429000-49447200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr3:49431200-49447200	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr3:49433800-49444000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr3:49433800-49447200	Weak transcription	Colonic Mucosa	Colon
11	chr3:49435400-49445600	Weak transcription	Fetal Brain Male	brain
12	chr3:49435400-49447000	Weak transcription	HSMMtube	muscle
13	chr3:49435400-49447800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:49435600-49443200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr3:49435800-49446800	Weak transcription	Brain Angular Gyrus	brain
16	chr3:49436600-49443200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr3:49438200-49443800	Weak transcription	K562	blood
18	chr3:49438200-49444000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr3:49438200-49446800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:49438800-49444000	Weak transcription	Right Ventricle	heart
21	chr3:49439000-49443200	Weak transcription	Primary B cells from cord blood	blood
22	chr3:49439000-49447200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr3:49439200-49443600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr3:49439400-49443400	Weak transcription	Brain Hippocampus Middle	brain
25	chr3:49439400-49444200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr3:49439600-49443200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr3:49439600-49443200	Weak transcription	Gastric	stomach
28	chr3:49439600-49443600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr3:49439600-49443600	Weak transcription	HepG2	liver
30	chr3:49439600-49444600	Weak transcription	Fetal Heart	heart
31	chr3:49439600-49447200	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr3:49439800-49444200	Weak transcription	Primary hematopoietic stem cells	blood
33	chr3:49439800-49447000	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr3:49440200-49443600	Weak transcription	Primary T cells from cord blood	blood
35	chr3:49440200-49447000	Weak transcription	Fetal Lung	lung
36	chr3:49441200-49443200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr3:49441400-49443200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr3:49441400-49447000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr3:49441400-49447000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr3:49441400-49447200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr3:49441600-49443200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr3:49441600-49443200	Weak transcription	A549	lung
43	chr3:49441600-49443200	Weak transcription	Hela-S3	cervix
44	chr3:49441600-49443800	Weak transcription	Spleen	Spleen
45	chr3:49441600-49443800	Weak transcription	HMEC	breast
46	chr3:49441600-49443800	Weak transcription	HUVEC	blood vessel
47	chr3:49441600-49446000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr3:49441600-49447000	Weak transcription	Fetal Brain Female	brain
49	chr3:49441600-49447200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr3:49441600-49447600	Weak transcription	Placenta Amnion	Placenta Amnion

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