Variant report

Variant	rs7713479
Chromosome Location	chr5:43577190-43577191
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	chr5:43569229..43570816-chr5:43575910..43577569,2	K562	blood:
2	chr5:43555603..43557203-chr5:43575638..43578155,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NNT-5	chr5:43571510-43577741	NONHSAT101320

Variant related genes	Relation type
ENSG00000172239	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10036954	1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[ASN][1000 genomes]
rs10038608	0.96[MEX][hapmap]
rs10042992	0.96[MEX][hapmap]
rs10053229	0.83[ASN][1000 genomes]
rs10055801	0.89[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs10057103	0.96[MEX][hapmap]
rs10058558	0.96[MEX][hapmap]
rs10059912	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10059993	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];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10061165	0.96[MEX][hapmap]
rs10065689	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10065863	0.96[MEX][hapmap]
rs10066408	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10068064	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10074682	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs10462051	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11949083	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];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11952832	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11958046	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12187908	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs12332560	0.94[ASN][1000 genomes]
rs12521249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12651879	0.92[ASN][1000 genomes]
rs12652547	0.96[MEX][hapmap]
rs12697457	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13189004	0.96[MEX][hapmap]
rs13189484	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13359906	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13360902	0.91[EUR][1000 genomes]
rs1366410	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]
rs1389868	1.00[JPT][hapmap]
rs1593971	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs2131998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2172763	0.95[MEX][hapmap]
rs28437972	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28606458	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3776423	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[ASN][1000 genomes]
rs3806870	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs4072918	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4072919	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4073848	0.96[MEX][hapmap]
rs4074777	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4331909	0.90[ASN][1000 genomes]
rs4367306	0.96[MEX][hapmap]
rs4386738	0.89[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4428418	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4467713	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[ASN][1000 genomes]
rs4535459	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4610465	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4866752	0.95[MEX][hapmap]
rs4866833	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[ASN][1000 genomes]
rs4866835	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55667604	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55855322	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56008952	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56097465	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56333629	0.83[EUR][1000 genomes]
rs57403343	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59001943	0.90[ASN][1000 genomes]
rs59224335	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60297702	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6451695	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs6451696	1.00[CHB][hapmap];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];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6451705	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap]
rs6451706	0.95[MEX][hapmap]
rs6451712	0.90[ASN][1000 genomes]
rs6451718	0.96[MEX][hapmap]
rs67261887	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67466542	0.83[ASN][1000 genomes]
rs67581152	0.92[ASN][1000 genomes]
rs6860493	0.94[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6862102	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6866325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6866802	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6869933	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6870018	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6878770	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs6884661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6885679	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6891363	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6895327	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6896693	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs6898866	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72756535	0.83[ASN][1000 genomes]
rs750582	0.96[MEX][hapmap]
rs750583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs754301	0.82[CHB][hapmap]
rs7703662	0.96[CEU][hapmap]
rs7705166	0.85[CHB][hapmap];0.98[AFR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7706431	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7708369	0.96[MEX][hapmap]
rs7710628	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7715782	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7717636	0.94[ASN][1000 genomes]
rs7718627	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs7732656	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]
rs7736108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7736615	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7737793	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9687341	0.85[ASN][1000 genomes]
rs9885189	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	esv3471239	chr5:43541792-43587904	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
5	esv3471240	chr5:43541792-43587904	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7713479	YY2	trans	cerebellum	SCAN
rs7713479	NNT	cis	lymphoblastoid	seeQTL
rs7713479	HSD11B1L	trans	cerebellum	SCAN
rs7713479	NNT	cis	cerebellum	SCAN
rs7713479	NNT	cis	multi-tissue	Pritchard
rs7713479	C5orf34	cis	parietal	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43557800-43584600	Weak transcription	Psoas Muscle	Psoas
2	chr5:43560200-43584400	Weak transcription	K562	blood
3	chr5:43564600-43580200	Weak transcription	Fetal Kidney	kidney
4	chr5:43565400-43579000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr5:43565400-43601800	Weak transcription	Fetal Thymus	thymus
6	chr5:43565600-43581800	Weak transcription	Dnd41	blood
7	chr5:43566200-43590400	Weak transcription	Thymus	Thymus
8	chr5:43566400-43580200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr5:43566800-43586000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr5:43567400-43602000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr5:43568000-43601800	Weak transcription	Primary B cells from peripheral blood	blood
12	chr5:43568000-43602400	Weak transcription	Pancreas	Pancrea
13	chr5:43568400-43581800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr5:43568600-43601800	Weak transcription	Fetal Brain Female	brain
15	chr5:43569000-43601400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr5:43569200-43591800	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr5:43570000-43582000	Weak transcription	Liver	Liver
18	chr5:43570200-43581600	Weak transcription	Left Ventricle	heart
19	chr5:43570200-43601800	Weak transcription	Right Ventricle	heart
20	chr5:43570600-43577200	Weak transcription	Primary B cells from cord blood	blood
21	chr5:43572000-43579600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr5:43572000-43591800	Weak transcription	Aorta	Aorta
23	chr5:43572000-43602400	Weak transcription	Ovary	ovary
24	chr5:43572400-43582600	Weak transcription	Primary hematopoietic stem cells	blood
25	chr5:43572600-43583400	Weak transcription	Stomach Smooth Muscle	stomach
26	chr5:43572800-43577400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr5:43572800-43582000	Weak transcription	Colon Smooth Muscle	Colon
28	chr5:43572800-43584400	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr5:43573000-43582200	Weak transcription	HSMMtube	muscle
30	chr5:43573000-43582400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr5:43573000-43582600	Weak transcription	Adipose Nuclei	Adipose
32	chr5:43573000-43601800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr5:43573000-43601800	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr5:43573400-43581600	Weak transcription	Fetal Muscle Trunk	muscle
35	chr5:43573600-43583200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr5:43573800-43579000	Weak transcription	Fetal Intestine Large	intestine
37	chr5:43573800-43584600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr5:43574000-43577200	Weak transcription	Hela-S3	cervix
39	chr5:43574000-43579200	Weak transcription	Duodenum Mucosa	Duodenum
40	chr5:43574000-43580600	Weak transcription	Lung	lung
41	chr5:43574000-43581800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr5:43574000-43583800	Weak transcription	Brain Angular Gyrus	brain
43	chr5:43574000-43601800	Weak transcription	Brain Anterior Caudate	brain
44	chr5:43574200-43582000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr5:43574400-43579000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr5:43574400-43582600	Weak transcription	Fetal Lung	lung
47	chr5:43574400-43600800	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr5:43574600-43577400	Weak transcription	Fetal Heart	heart
49	chr5:43574800-43577600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr5:43575000-43577200	Strong transcription	Fetal Stomach	stomach

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