Variant report

Variant	rs1366410
Chromosome Location	chr5:43601610-43601611
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ARID3A	chr5:43601601-43602478	K562	blood:	n/a	n/a
2	MXI1	chr5:43601361-43604702	SK-N-SH	brain:	n/a	n/a
3	FOXA1	chr5:43601598-43602021	HepG2	liver:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:43599927..43602440-chr5:43629272..43630773,2	MCF-7	breast:
2	chr5:43554854..43559895-chr5:43599481..43606699,15	MCF-7	breast:
3	chr5:43482042..43485833-chr5:43601604..43604541,3	MCF-7	breast:
4	chr5:43067084..43070080-chr5:43601534..43603658,2	K562	blood:
5	chr5:43599902..43602064-chr5:43626032..43628822,2	K562	blood:
6	chr5:43555487..43559521-chr5:43598404..43605405,16	K562	blood:
7	chr5:43120124..43122141-chr5:43601364..43602944,2	K562	blood:
8	chr5:43487601..43489492-chr5:43600088..43602160,2	K562	blood:
9	chr5:43541229..43543256-chr5:43600683..43602539,2	K562	blood:
10	chr5:43552832..43560830-chr5:43598877..43605844,26	MCF-7	breast:
11	chr5:43482483..43486113-chr5:43601084..43606081,7	K562	blood:
12	chr5:43540433..43542729-chr5:43600683..43602719,2	K562	blood:
13	chr5:43513363..43516571-chr5:43601265..43603524,3	K562	blood:
14	chr5:43555382..43559666-chr5:43598979..43604929,17	K562	blood:

No data

Variant related genes	Relation type
NNT	TF binding region
ENSG00000177738	Chromatin interaction
ENSG00000151881	Chromatin interaction
ENSG00000248240	Chromatin interaction
ENSG00000172239	Chromatin interaction
ENSG00000172244	Chromatin interaction
ENSG00000172262	Chromatin interaction
ENSG00000249492	Chromatin interaction

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	0.83[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap]
rs10057103	0.96[MEX][hapmap]
rs10058558	0.96[MEX][hapmap]
rs10059912	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10059993	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];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10061165	0.96[MEX][hapmap]
rs10065689	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[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];0.85[ASN][1000 genomes]
rs11949083	0.89[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11952832	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11958046	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12187908	0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs12332560	0.85[ASN][1000 genomes]
rs12521249	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12651879	0.83[ASN][1000 genomes]
rs12652547	0.96[MEX][hapmap]
rs12697457	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13189004	0.96[MEX][hapmap]
rs13189484	0.81[EUR][1000 genomes]
rs13359906	0.84[EUR][1000 genomes];0.85[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	0.81[ASN][1000 genomes]
rs28606458	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[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	0.83[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.91[TSI][hapmap];0.81[ASN][1000 genomes]
rs4072919	0.83[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.81[ASN][1000 genomes]
rs4073848	0.96[MEX][hapmap]
rs4074777	0.83[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs4331909	0.81[ASN][1000 genomes]
rs4367306	0.96[MEX][hapmap]
rs4386738	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4428418	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4467713	0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[ASN][1000 genomes]
rs4535459	0.92[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];0.85[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];0.81[ASN][1000 genomes]
rs4866835	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55667604	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55855322	0.81[ASN][1000 genomes]
rs56008952	0.83[EUR][1000 genomes]
rs56097465	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59001943	0.81[ASN][1000 genomes]
rs59224335	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60297702	0.81[EUR][1000 genomes];0.81[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	0.83[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs6451706	0.95[MEX][hapmap]
rs6451712	0.81[ASN][1000 genomes]
rs6451718	0.96[MEX][hapmap]
rs67261887	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67581152	0.83[ASN][1000 genomes]
rs6860493	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[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];0.81[ASN][1000 genomes]
rs6866802	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6869933	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6870018	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6878770	0.83[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs6884661	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6885679	0.83[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];0.91[TSI][hapmap]
rs6891363	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6895327	0.83[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs6896693	0.83[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs6898866	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[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	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7706431	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7708369	0.96[MEX][hapmap]
rs7710628	0.83[ASW][hapmap];0.96[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]
rs7713479	0.94[ASW][hapmap];1.00[CEU][hapmap];0.82[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];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7715782	0.83[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7717636	0.85[ASN][1000 genomes]
rs7718627	0.83[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.91[TSI][hapmap]
rs7732656	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]
rs7736108	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7736615	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7737793	0.84[EUR][1000 genomes]
rs9885189	0.84[EUR][1000 genomes];0.85[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
rs1366410	NNT	Cis_1M	lymphoblastoid	RTeQTL
rs1366410	HSD11B1L	trans	cerebellum	SCAN
rs1366410	YY2	trans	cerebellum	SCAN
rs1366410	NNT	cis	multi-tissue	Pritchard
rs1366410	C5orf34	cis	parietal	SCAN
rs1366410	NNT	cis	lymphoblastoid	seeQTL
rs1366410	NNT	cis	cerebellum	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

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	chr5:43570200-43601800	Weak transcription	Right Ventricle	heart
7	chr5:43572000-43602400	Weak transcription	Ovary	ovary
8	chr5:43573000-43601800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr5:43573000-43601800	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr5:43574000-43601800	Weak transcription	Brain Anterior Caudate	brain
11	chr5:43577200-43601800	Weak transcription	Fetal Stomach	stomach
12	chr5:43579400-43601800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr5:43582400-43601800	Weak transcription	Fetal Muscle Trunk	muscle
14	chr5:43582800-43601800	Weak transcription	Fetal Intestine Large	intestine
15	chr5:43583400-43601800	Weak transcription	Fetal Lung	lung
16	chr5:43583800-43601800	Weak transcription	Primary T cells from cord blood	blood
17	chr5:43592600-43601800	Weak transcription	Fetal Muscle Leg	muscle
18	chr5:43596000-43601800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr5:43598000-43601800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr5:43598800-43602000	Weak transcription	Gastric	stomach
21	chr5:43599600-43601800	Weak transcription	Stomach Mucosa	stomach
22	chr5:43600000-43601800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr5:43600000-43601800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr5:43600200-43601800	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr5:43600400-43601800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr5:43600400-43601800	Weak transcription	Aorta	Aorta
27	chr5:43600400-43601800	Weak transcription	Left Ventricle	heart
28	chr5:43600600-43601800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr5:43600600-43601800	Enhancers	Liver	Liver
30	chr5:43600800-43601800	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr5:43600800-43601800	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr5:43600800-43602000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr5:43600800-43602000	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr5:43600800-43602000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr5:43600800-43604800	Active TSS	Psoas Muscle	Psoas
36	chr5:43600800-43605200	Active TSS	Right Atrium	heart
37	chr5:43601000-43601800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr5:43601000-43601800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr5:43601000-43601800	Enhancers	Muscle Satellite Cultured Cells	--
40	chr5:43601000-43601800	Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr5:43601000-43602000	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr5:43601000-43602000	Weak transcription	Fetal Kidney	kidney
43	chr5:43601200-43601800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr5:43601200-43603600	Active TSS	K562	blood
45	chr5:43601400-43601800	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr5:43601400-43601800	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr5:43601400-43601800	Enhancers	Fetal Intestine Small	intestine
48	chr5:43601400-43601800	Enhancers	Rectal Smooth Muscle	rectum
49	chr5:43601400-43601800	Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr5:43601400-43601800	Enhancers	A549	lung

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