Variant report

Variant	rs7644148
Chromosome Location	chr3:49545241-49545242
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr3:49545072-49545273	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49506496..49509240-chr3:49545063..49547499,2	MCF-7	breast:
2	chr3:49539771..49542483-chr3:49542652..49545389,2	MCF-7	breast:

Variant related genes	Relation type
DAG1	TF binding region
ENSG00000173402	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 34 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs1009051	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10155014	0.84[EUR][1000 genomes]
rs10452032	0.82[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.97[MKK][hapmap];0.91[YRI][hapmap]
rs1078341	0.82[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap]
rs10865956	1.00[ASW][hapmap];1.00[CEU][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];0.95[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1106620	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11130190	0.82[EUR][1000 genomes]
rs11130204	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11130207	0.87[AFR][1000 genomes]
rs11130208	0.91[ASW][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes]
rs11130217	0.82[ASW][hapmap];1.00[CHD][hapmap];0.88[LWK][hapmap];0.98[MKK][hapmap];0.91[YRI][hapmap]
rs11709734	1.00[CHD][hapmap]
rs11715060	0.80[EUR][1000 genomes]
rs11719762	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs11720657	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs11928090	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12583	1.00[ASW][hapmap];1.00[CEU][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];0.95[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12637313	1.00[CHD][hapmap];0.91[YRI][hapmap]
rs13096474	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]
rs13096480	0.87[YRI][hapmap]
rs13322887	1.00[ASW][hapmap];1.00[CEU][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];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1352889	1.00[CHD][hapmap];0.84[LWK][hapmap];0.95[MKK][hapmap]
rs1464569	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs1491983	0.82[ASW][hapmap];1.00[CHD][hapmap];0.86[LWK][hapmap];0.95[MKK][hapmap]
rs1532204	0.90[AFR][1000 genomes]
rs1586827	0.91[YRI][hapmap]
rs1982861	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2029591	0.91[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.91[YRI][hapmap]
rs2131108	0.82[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.91[YRI][hapmap]
rs2140270	1.00[ASW][hapmap];1.00[CEU][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];0.84[EUR][1000 genomes]
rs2177268	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs2312462	1.00[ASW][hapmap];1.00[CEU][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];0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2329021	0.82[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.91[YRI][hapmap]
rs2329025	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3020779	0.82[YRI][hapmap]
rs3448	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs34890793	1.00[CHD][hapmap];0.83[LWK][hapmap];0.92[MKK][hapmap]
rs3866330	1.00[CEU][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];0.94[EUR][1000 genomes]
rs3870339	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3870341	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3905330	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];0.98[EUR][1000 genomes]
rs4052546	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4241405	0.91[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.91[YRI][hapmap]
rs4241407	1.00[ASW][hapmap];1.00[CEU][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];0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4855833	1.00[CHD][hapmap];0.84[LWK][hapmap];0.95[MKK][hapmap]
rs4855837	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4855845	0.90[YRI][hapmap]
rs4855846	0.82[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.91[YRI][hapmap]
rs4855853	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4855858	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4855869	0.86[EUR][1000 genomes]
rs4855882	1.00[CHD][hapmap]
rs4855885	1.00[CHD][hapmap]
rs4955430	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.81[EUR][1000 genomes]
rs56049603	0.81[EUR][1000 genomes]
rs56127630	0.84[EUR][1000 genomes]
rs56324858	0.85[EUR][1000 genomes]
rs57273516	0.90[EUR][1000 genomes]
rs62259933	0.89[EUR][1000 genomes]
rs62259943	0.83[EUR][1000 genomes]
rs62259944	0.80[EUR][1000 genomes]
rs62259947	0.84[EUR][1000 genomes]
rs62261183	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62261249	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6446262	0.80[EUR][1000 genomes]
rs6446275	0.89[EUR][1000 genomes]
rs6446284	0.80[AFR][1000 genomes]
rs6446285	1.00[CHD][hapmap]
rs6769744	0.81[EUR][1000 genomes]
rs6774202	1.00[CHD][hapmap];0.84[LWK][hapmap];0.94[MKK][hapmap]
rs6783003	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6785045	0.84[EUR][1000 genomes]
rs6797299	0.94[YRI][hapmap];0.90[AFR][1000 genomes]
rs6805609	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs72934271	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73088137	0.86[EUR][1000 genomes]
rs7355800	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7374731	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7613491	0.96[EUR][1000 genomes]
rs7619789	0.90[EUR][1000 genomes]
rs7620024	0.86[EUR][1000 genomes]
rs7622786	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7625857	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7638750	0.80[EUR][1000 genomes]
rs7647973	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7648995	0.84[EUR][1000 genomes]
rs7651372	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7653505	1.00[CHD][hapmap];0.84[MKK][hapmap]
rs8897	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs940045	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]
rs9654010	0.86[EUR][1000 genomes]
rs974495	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];0.81[EUR][1000 genomes]
rs9757181	1.00[CEU][hapmap]
rs9809237	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9817807	0.83[EUR][1000 genomes]
rs9824435	1.00[CHD][hapmap]
rs9842132	0.83[EUR][1000 genomes]
rs9860055	1.00[ASW][hapmap];1.00[CEU][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];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9861027	0.84[EUR][1000 genomes]
rs9862534	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9871024	1.00[ASW][hapmap];1.00[CEU][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];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9881860	1.00[CEU][hapmap]
rs9883000	0.82[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.91[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834687	chr3:49448632-49631788	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:34)

SNP	Gene	Cis/trans	Tissue	Source
rs7644148	AMT	cis	Whole Blood	GTEx
rs7644148	NICN1-AS1	cis	Thyroid	GTEx
rs7644148	AMT	cis	Esophagus Muscularis	GTEx
rs7644148	SEMA3G	cis	cerebellum	SCAN
rs7644148	AMT	cis	Skin Sun Exposed Lower leg	GTEx
rs7644148	GMPPB	cis	parietal	SCAN
rs7644148	AMT	cis	Esophagus Mucosa	GTEx
rs7644148	AMT	cis	Adipose Subcutaneous	GTEx
rs7644148	WDR6	cis	parietal	SCAN
rs7644148	AMT	cis	Thyroid	GTEx
rs7644148	WDR6	cis	Nerve Tibial	GTEx
rs7644148	NME6	cis	cerebellum	SCAN
rs7644148	WDR6	cis	Muscle Skeletal	GTEx
rs7644148	AMT	cis	Muscle Skeletal	GTEx
rs7644148	LZTFL1	cis	cerebellum	SCAN
rs7644148	P4HTM	cis	parietal	SCAN
rs7644148	AMT	cis	Artery Aorta	GTEx
rs7644148	AMT	cis	Artery Tibial	GTEx
rs7644148	QRICH1	cis	cerebellum	SCAN
rs7644148	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs7644148	AMT	cis	parietal	SCAN
rs7644148	AMT	cis	lung	GTEx
rs7644148	GNL3	cis	cerebellum	SCAN
rs7644148	DALRD3	cis	parietal	SCAN
rs7644148	NICN1	cis	cerebellum	SCAN
rs7644148	AMT	cis	cerebellum	SCAN
rs7644148	GPX1	cis	parietal	SCAN
rs7644148	AMT	cis	lymphoblastoid	seeQTL
rs7644148	ZNF589	cis	parietal	SCAN
rs7644148	NICN1	cis	Thyroid	GTEx
rs7644148	WDR6	cis	cerebellum	SCAN
rs7644148	DALRD3	cis	cerebellum	SCAN
rs7644148	WDR6	cis	Esophagus Muscularis	GTEx
rs7644148	AMT	cis	Nerve Tibial	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49509800-49547800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr3:49510000-49547800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:49514600-49548000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr3:49515400-49547800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:49515400-49547800	Weak transcription	Fetal Brain Female	brain
6	chr3:49515400-49548800	Weak transcription	Esophagus	oesophagus
7	chr3:49517000-49547800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr3:49517200-49547800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr3:49522200-49547800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr3:49522400-49548000	Weak transcription	Spleen	Spleen
11	chr3:49523400-49548000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:49523400-49548000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr3:49523600-49548200	Weak transcription	Brain Substantia Nigra	brain
14	chr3:49526000-49547800	Weak transcription	Dnd41	blood
15	chr3:49526000-49548000	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr3:49527600-49547800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr3:49529600-49568600	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr3:49530400-49547800	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr3:49531000-49548000	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr3:49531200-49547800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr3:49531400-49547600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr3:49531400-49547800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr3:49531400-49547800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:49531400-49547800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr3:49531600-49547800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr3:49531600-49547800	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr3:49531600-49547800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:49531800-49547400	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr3:49531800-49547800	Weak transcription	Brain Germinal Matrix	brain
30	chr3:49533000-49547800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr3:49533000-49547800	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr3:49533000-49547800	Weak transcription	Ovary	ovary
33	chr3:49533000-49547800	Weak transcription	GM12878-XiMat	blood
34	chr3:49533800-49547800	Weak transcription	Thymus	Thymus
35	chr3:49536600-49548000	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr3:49538000-49548000	Weak transcription	Lung	lung
37	chr3:49538000-49554800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr3:49538200-49548000	Weak transcription	Fetal Lung	lung
39	chr3:49538200-49548000	Weak transcription	Left Ventricle	heart
40	chr3:49538200-49550600	Weak transcription	Colonic Mucosa	Colon
41	chr3:49538400-49547600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:49538400-49547800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr3:49538400-49547800	Weak transcription	Gastric	stomach
44	chr3:49538400-49547800	Weak transcription	Right Ventricle	heart
45	chr3:49538400-49548000	Weak transcription	Brain Cingulate Gyrus	brain
46	chr3:49538600-49547800	Weak transcription	Fetal Thymus	thymus
47	chr3:49538600-49547800	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr3:49538600-49548000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr3:49538600-49548000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr3:49538600-49548800	Weak transcription	Rectal Smooth Muscle	rectum

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