Variant report

Variant	rs7732656
Chromosome Location	chr5:43593124-43593125
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	GATA3	chr5:43592906-43593189	SH-SY5Y	brain:	n/a	n/a
2	CTCF	chr5:43593020-43593170	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:43552652..43554518-chr5:43592986..43594640,2	K562	blood:

Variant related genes	Relation type
ENSG00000249286	TF binding region

Extended variants
information (count: 98 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10036954	0.82[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs10038608	0.96[MEX][hapmap]
rs10042992	0.96[MEX][hapmap]
rs10055801	0.89[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap]
rs10057103	0.96[MEX][hapmap]
rs10058558	0.96[MEX][hapmap]
rs10059912	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10059993	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10061165	0.96[MEX][hapmap]
rs10065689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10065863	0.96[MEX][hapmap]
rs10068064	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10074682	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs10462051	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11949083	0.84[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11952832	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11958046	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12187908	0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs12332560	0.88[ASN][1000 genomes]
rs12521249	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12651879	0.86[ASN][1000 genomes]
rs12652547	0.96[MEX][hapmap]
rs12697457	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13189004	0.96[MEX][hapmap]
rs13189484	0.81[EUR][1000 genomes]
rs13359906	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1366410	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1389868	1.00[JPT][hapmap]
rs1593971	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap]
rs2131998	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2172763	0.96[MEX][hapmap]
rs28437972	0.84[ASN][1000 genomes]
rs28606458	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3776423	0.82[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs3806870	1.00[JPT][hapmap];0.91[MEX][hapmap]
rs4072918	0.89[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[ASN][1000 genomes]
rs4072919	0.89[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.84[ASN][1000 genomes]
rs4073848	0.96[MEX][hapmap]
rs4074777	0.89[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs4331909	0.84[ASN][1000 genomes]
rs4367306	0.96[MEX][hapmap]
rs4386738	0.89[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4428418	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4467713	0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[ASN][1000 genomes]
rs4535459	0.92[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4610465	0.81[EUR][1000 genomes]
rs4866752	0.95[MEX][hapmap]
rs4866833	0.82[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[ASN][1000 genomes]
rs4866835	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55667604	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55855322	0.84[ASN][1000 genomes]
rs56008952	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56097465	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59001943	0.84[ASN][1000 genomes]
rs59224335	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60297702	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6451695	0.82[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs6451696	0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs6451697	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6451698	0.86[JPT][hapmap];0.87[MEX][hapmap]
rs6451699	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6451705	0.89[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap]
rs6451706	0.95[MEX][hapmap]
rs6451712	0.84[ASN][1000 genomes]
rs6451718	0.96[MEX][hapmap]
rs67261887	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67581152	0.86[ASN][1000 genomes]
rs6860493	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6862102	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6866325	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6866802	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6869933	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6870018	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6878770	0.89[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs6884661	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6885679	0.89[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs6891363	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6895327	0.89[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs6896693	0.89[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs6898866	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs750582	0.96[MEX][hapmap]
rs750583	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7703662	0.96[CEU][hapmap]
rs7705166	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7706431	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7708369	0.96[MEX][hapmap]
rs7710628	0.89[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap]
rs7713479	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7715782	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7717636	0.88[ASN][1000 genomes]
rs7718627	0.89[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs7736108	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7736615	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7737793	0.83[EUR][1000 genomes]
rs9885189	0.83[EUR][1000 genomes];0.88[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	nsv881017	chr5:43444826-43731692	Weak transcription Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	222 gene(s)	inside rSNPs	diseases
2	nsv830275	chr5:43469511-43639384	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	220 gene(s)	inside rSNPs	diseases
3	nsv881108	chr5:43527432-43800333	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7732656	NNT	cis	lymphoblastoid	seeQTL
rs7732656	NNT	Cis_1M	lymphoblastoid	RTeQTL
rs7732656	HSD11B1L	trans	cerebellum	SCAN
rs7732656	NNT	cis	multi-tissue	Pritchard
rs7732656	NNT	cis	cerebellum	SCAN
rs7732656	YY2	trans	cerebellum	SCAN
rs7732656	C5orf34	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43565400-43601800	Weak transcription	Fetal Thymus	thymus
2	chr5:43567400-43602000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr5:43568000-43601800	Weak transcription	Primary B cells from peripheral blood	blood
4	chr5:43568000-43602400	Weak transcription	Pancreas	Pancrea
5	chr5:43568600-43601800	Weak transcription	Fetal Brain Female	brain
6	chr5:43569000-43601400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr5:43570200-43601800	Weak transcription	Right Ventricle	heart
8	chr5:43572000-43602400	Weak transcription	Ovary	ovary
9	chr5:43573000-43601800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr5:43573000-43601800	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr5:43574000-43601800	Weak transcription	Brain Anterior Caudate	brain
12	chr5:43574400-43600800	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr5:43575000-43601400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr5:43576400-43601400	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr5:43577200-43601800	Weak transcription	Fetal Stomach	stomach
16	chr5:43577600-43601600	Weak transcription	Primary B cells from cord blood	blood
17	chr5:43579400-43601800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr5:43582000-43600600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr5:43582400-43601800	Weak transcription	Fetal Muscle Trunk	muscle
20	chr5:43582800-43597800	Weak transcription	Liver	Liver
21	chr5:43582800-43601800	Weak transcription	Fetal Intestine Large	intestine
22	chr5:43583000-43599800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr5:43583400-43601600	Weak transcription	Primary hematopoietic stem cells	blood
24	chr5:43583400-43601800	Weak transcription	Fetal Lung	lung
25	chr5:43583600-43600600	Weak transcription	Dnd41	blood
26	chr5:43583800-43601800	Weak transcription	Primary T cells from cord blood	blood
27	chr5:43585000-43600600	Weak transcription	K562	blood
28	chr5:43585600-43598200	Weak transcription	Psoas Muscle	Psoas
29	chr5:43585600-43599800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr5:43588400-43601400	Weak transcription	Fetal Intestine Small	intestine
31	chr5:43589400-43599600	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr5:43589600-43601600	Weak transcription	Fetal Brain Male	brain
33	chr5:43589800-43599600	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr5:43590600-43600400	Weak transcription	HepG2	liver
35	chr5:43591600-43593400	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr5:43591800-43593200	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr5:43592200-43593400	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr5:43592200-43595400	Weak transcription	Left Ventricle	heart
39	chr5:43592200-43600000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr5:43592400-43593200	Enhancers	GM12878-XiMat	blood
41	chr5:43592600-43593600	Flanking Active TSS	Fetal Heart	heart
42	chr5:43592600-43601800	Weak transcription	Fetal Muscle Leg	muscle
43	chr5:43593000-43601400	Weak transcription	NHLF	lung

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