Variant report

Variant	rs7713458
Chromosome Location	chr5:43637233-43637234
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:43636622..43638460-chr5:43641354..43643193,2	K562	blood:

Extended variants
information (count: 148 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:144)

rs_ID	r²[population]
rs10042852	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10055801	0.84[YRI][hapmap]
rs10058080	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs10068064	0.84[YRI][hapmap]
rs10068765	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10069201	1.00[ASW][hapmap];0.85[LWK][hapmap];0.80[YRI][hapmap]
rs10074229	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10077102	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10461740	0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs10461741	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10461743	0.98[ASN][1000 genomes]
rs10461744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10462052	0.90[ASN][1000 genomes]
rs10462053	0.98[ASN][1000 genomes]
rs10462054	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10941642	0.87[CHD][hapmap];0.82[JPT][hapmap]
rs12654258	0.88[ASN][1000 genomes]
rs12656650	1.00[JPT][hapmap]
rs12657635	1.00[JPT][hapmap]
rs12659627	0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs13155888	1.00[JPT][hapmap]
rs13158796	0.90[ASN][1000 genomes]
rs13161149	0.83[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[ASN][1000 genomes]
rs13161298	0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs13161838	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13165869	1.00[JPT][hapmap]
rs13166593	0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13168053	1.00[JPT][hapmap]
rs13170672	0.94[ASN][1000 genomes]
rs13173498	0.94[ASN][1000 genomes]
rs13173517	1.00[JPT][hapmap]
rs13175688	0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs13177107	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs13181483	0.94[ASN][1000 genomes]
rs13183122	0.94[ASN][1000 genomes]
rs13186372	0.90[ASN][1000 genomes]
rs13187073	0.88[ASN][1000 genomes]
rs13187313	0.90[ASN][1000 genomes]
rs13188640	0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs13188683	0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs13189630	0.94[ASN][1000 genomes]
rs13356232	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1469436	0.94[ASN][1000 genomes]
rs16873404	0.83[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs16873421	0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs16873432	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16873433	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs16873435	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16873438	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16873443	0.94[ASN][1000 genomes]
rs16873454	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs16873455	0.94[ASN][1000 genomes]
rs16873466	0.94[ASN][1000 genomes]
rs16873502	1.00[MEX][hapmap]
rs2042950	1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[ASN][1000 genomes]
rs2131998	0.84[YRI][hapmap]
rs34076603	0.98[ASN][1000 genomes]
rs34079397	0.94[ASN][1000 genomes]
rs34153332	0.94[ASN][1000 genomes]
rs34225966	0.98[ASN][1000 genomes]
rs34307136	0.94[ASN][1000 genomes]
rs34330393	0.94[ASN][1000 genomes]
rs34361701	0.94[ASN][1000 genomes]
rs34361740	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34369923	0.98[ASN][1000 genomes]
rs34577568	0.94[ASN][1000 genomes]
rs34753533	0.98[ASN][1000 genomes]
rs34760245	0.98[ASN][1000 genomes]
rs34784550	0.98[ASN][1000 genomes]
rs34985223	0.94[ASN][1000 genomes]
rs35023717	0.86[ASN][1000 genomes]
rs35069805	0.98[ASN][1000 genomes]
rs35141665	0.94[ASN][1000 genomes]
rs35201656	0.90[ASN][1000 genomes]
rs35370110	0.94[ASN][1000 genomes]
rs35393262	0.85[ASN][1000 genomes]
rs35493041	0.88[ASN][1000 genomes]
rs35768478	0.98[ASN][1000 genomes]
rs35773835	0.94[ASN][1000 genomes]
rs35826690	0.90[ASN][1000 genomes]
rs35910245	0.94[ASN][1000 genomes]
rs35979310	0.90[ASN][1000 genomes]
rs3764979	0.98[ASN][1000 genomes]
rs3764980	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[ASN][1000 genomes]
rs3792915	0.94[ASN][1000 genomes]
rs3792916	0.94[ASN][1000 genomes]
rs3792917	0.83[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3792918	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3792921	0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3792922	0.94[ASN][1000 genomes]
rs3805720	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[ASN][1000 genomes]
rs3805721	0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3805722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3805723	0.94[ASN][1000 genomes]
rs3828695	0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4072918	0.84[YRI][hapmap]
rs4072919	0.84[YRI][hapmap]
rs4074777	0.84[YRI][hapmap]
rs41271083	0.94[ASN][1000 genomes]
rs4386738	0.84[YRI][hapmap]
rs4533897	1.00[JPT][hapmap]
rs62367607	0.90[ASN][1000 genomes]
rs62367633	0.92[ASN][1000 genomes]
rs62367649	0.94[ASN][1000 genomes]
rs62367650	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62367651	0.94[ASN][1000 genomes]
rs62367653	0.89[ASN][1000 genomes]
rs62368560	0.87[EUR][1000 genomes]
rs62368561	0.94[ASN][1000 genomes]
rs62368564	0.94[ASN][1000 genomes]
rs62368566	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62368567	0.94[ASN][1000 genomes]
rs62368570	0.94[ASN][1000 genomes]
rs62368571	0.94[ASN][1000 genomes]
rs62368594	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6451697	0.84[YRI][hapmap]
rs6451699	0.84[YRI][hapmap]
rs6451705	0.84[YRI][hapmap]
rs6451719	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[ASN][1000 genomes]
rs6451720	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6862487	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6863699	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6868763	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6875118	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6878770	0.84[YRI][hapmap]
rs6885679	0.84[YRI][hapmap]
rs6893250	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6895327	0.84[YRI][hapmap]
rs6896693	0.84[YRI][hapmap]
rs6896932	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6898436	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71590644	0.98[ASN][1000 genomes]
rs71590645	0.98[ASN][1000 genomes]
rs71629182	0.98[ASN][1000 genomes]
rs71629184	0.94[ASN][1000 genomes]
rs71629185	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71629186	0.94[ASN][1000 genomes]
rs71629187	0.94[ASN][1000 genomes]
rs7710628	0.84[YRI][hapmap]
rs7713749	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7716562	0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7718627	0.84[YRI][hapmap]
rs7736108	0.84[YRI][hapmap]
rs7737947	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv980970	chr5:43636826-43643825	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7713458	NNT	cis	lymphoblastoid	seeQTL
rs7713458	NNT	cis	multi-tissue	Pritchard
rs7713458	NNT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43604400-43649200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:43604400-43649200	Weak transcription	Esophagus	oesophagus
3	chr5:43604400-43660600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:43604600-43649800	Weak transcription	Colonic Mucosa	Colon
5	chr5:43604800-43649800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr5:43605000-43656000	Weak transcription	Small Intestine	intestine
7	chr5:43606800-43648200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr5:43608400-43640600	Strong transcription	Dnd41	blood
9	chr5:43610800-43649400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr5:43612600-43649400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr5:43612800-43647400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr5:43613400-43645400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr5:43613800-43646200	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr5:43614000-43647600	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr5:43616000-43648200	Weak transcription	HepG2	liver
16	chr5:43619000-43642800	Weak transcription	Fetal Brain Male	brain
17	chr5:43620200-43650600	Weak transcription	Placenta	Placenta
18	chr5:43621200-43650200	Weak transcription	NHEK	skin
19	chr5:43621600-43651800	Weak transcription	HMEC	breast
20	chr5:43621800-43667400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr5:43622200-43648200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr5:43623400-43645400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr5:43624200-43649200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr5:43628200-43638400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr5:43629000-43644400	Weak transcription	Fetal Intestine Small	intestine
26	chr5:43630000-43638200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr5:43630200-43648800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr5:43630200-43658800	Weak transcription	Stomach Mucosa	stomach
29	chr5:43630600-43640800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr5:43631000-43638200	Strong transcription	Fetal Thymus	thymus
31	chr5:43631000-43638200	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr5:43631000-43640600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr5:43631200-43638000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr5:43631600-43637600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr5:43631600-43637600	Weak transcription	Lung	lung
36	chr5:43631600-43638200	Strong transcription	Fetal Muscle Leg	muscle
37	chr5:43631600-43638400	Strong transcription	Fetal Muscle Trunk	muscle
38	chr5:43631600-43642200	Weak transcription	Brain Hippocampus Middle	brain
39	chr5:43631600-43649200	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr5:43631600-43651400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr5:43631600-43664200	Weak transcription	A549	lung
42	chr5:43632200-43638000	Strong transcription	Primary hematopoietic stem cells	blood
43	chr5:43633000-43649200	Weak transcription	Ovary	ovary
44	chr5:43633200-43642200	Weak transcription	Osteobl	bone
45	chr5:43633200-43642400	Weak transcription	Brain Anterior Caudate	brain
46	chr5:43633200-43643200	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr5:43633200-43644600	Weak transcription	NH-A	brain
48	chr5:43633600-43642200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr5:43633800-43640000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr5:43633800-43648600	Weak transcription	Fetal Stomach	stomach

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