Variant report

Variant	rs16873438
Chromosome Location	chr5:43648914-43648915
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:43646050..43649875-chr5:43653093..43656688,3	K562	blood:
2	chr5:43555714..43557829-chr5:43647823..43651133,3	K562	blood:
3	chr5:43643698..43645571-chr5:43647494..43649590,2	K562	blood:
4	chr5:43643742..43646720-chr5:43647834..43650094,2	K562	blood:

Variant related genes	Relation type
ENSG00000112992	Chromatin interaction
ENSG00000172239	Chromatin interaction

Extended variants
information (count: 149 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:147)

rs_ID	r²[population]
rs10042852	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10055801	0.84[YRI][hapmap]
rs10058080	0.82[JPT][hapmap]
rs10068064	0.86[YRI][hapmap]
rs10068765	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10069201	0.80[YRI][hapmap]
rs10069341	0.83[EUR][1000 genomes]
rs10074229	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10077102	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10155531	0.80[EUR][1000 genomes]
rs10461741	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10461743	0.94[ASN][1000 genomes]
rs10461744	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10462052	0.87[ASN][1000 genomes]
rs10462053	0.94[ASN][1000 genomes]
rs10462054	0.82[JPT][hapmap];0.98[ASN][1000 genomes]
rs11737988	0.83[EUR][1000 genomes]
rs12654258	0.85[ASN][1000 genomes]
rs12656650	0.82[JPT][hapmap]
rs13158796	0.87[ASN][1000 genomes]
rs13161149	0.90[ASN][1000 genomes]
rs13161298	0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs13161838	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13165869	0.82[JPT][hapmap]
rs13166593	0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs13168053	0.82[JPT][hapmap]
rs13170672	0.98[ASN][1000 genomes]
rs13173498	0.98[ASN][1000 genomes]
rs13173517	0.82[JPT][hapmap]
rs13175688	0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs13177107	0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs13181483	0.98[ASN][1000 genomes]
rs13183122	0.98[ASN][1000 genomes]
rs13186372	0.87[ASN][1000 genomes]
rs13187073	0.85[ASN][1000 genomes]
rs13187313	0.87[ASN][1000 genomes]
rs13188640	0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs13188683	0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs13189630	0.98[ASN][1000 genomes]
rs13356232	1.00[CEU][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1469436	0.98[ASN][1000 genomes]
rs16873404	0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs16873421	0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs16873432	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16873433	1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs16873435	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16873443	0.98[ASN][1000 genomes]
rs16873454	0.82[JPT][hapmap];0.98[ASN][1000 genomes]
rs16873455	0.98[ASN][1000 genomes]
rs16873466	0.98[ASN][1000 genomes]
rs2042950	0.85[ASN][1000 genomes]
rs2131998	0.86[YRI][hapmap]
rs34076603	0.94[ASN][1000 genomes]
rs34079397	0.98[ASN][1000 genomes]
rs34153332	0.90[ASN][1000 genomes]
rs34225966	0.94[ASN][1000 genomes]
rs34307136	0.98[ASN][1000 genomes]
rs34325384	0.83[EUR][1000 genomes]
rs34330393	0.90[ASN][1000 genomes]
rs34361701	0.98[ASN][1000 genomes]
rs34361740	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34369923	0.94[ASN][1000 genomes]
rs34577568	0.90[ASN][1000 genomes]
rs34753533	0.94[ASN][1000 genomes]
rs34760245	0.94[ASN][1000 genomes]
rs34784550	0.94[ASN][1000 genomes]
rs34985223	0.98[ASN][1000 genomes]
rs35023717	0.90[ASN][1000 genomes]
rs35069805	0.94[ASN][1000 genomes]
rs35072002	0.83[EUR][1000 genomes]
rs35141665	0.98[ASN][1000 genomes]
rs35201656	0.87[ASN][1000 genomes]
rs35370110	0.98[ASN][1000 genomes]
rs35383935	0.83[EUR][1000 genomes]
rs35393262	0.81[ASN][1000 genomes]
rs35493041	0.85[ASN][1000 genomes]
rs35697559	0.83[EUR][1000 genomes]
rs35768478	0.94[ASN][1000 genomes]
rs35773835	0.90[ASN][1000 genomes]
rs35826690	0.87[ASN][1000 genomes]
rs35867146	0.83[EUR][1000 genomes]
rs35910245	0.98[ASN][1000 genomes]
rs35979310	0.87[ASN][1000 genomes]
rs3764979	0.94[ASN][1000 genomes]
rs3764980	0.94[ASN][1000 genomes]
rs3792915	0.90[ASN][1000 genomes]
rs3792916	0.90[ASN][1000 genomes]
rs3792917	0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs3792918	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3792921	0.98[ASN][1000 genomes]
rs3792922	0.98[ASN][1000 genomes]
rs3805720	0.98[ASN][1000 genomes]
rs3805721	0.82[JPT][hapmap];0.98[ASN][1000 genomes]
rs3805722	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805723	0.98[ASN][1000 genomes]
rs3828695	0.82[JPT][hapmap];0.98[ASN][1000 genomes]
rs4072918	0.84[YRI][hapmap]
rs4072919	0.84[YRI][hapmap]
rs4074777	0.84[YRI][hapmap]
rs41271083	0.98[ASN][1000 genomes]
rs4386738	0.84[YRI][hapmap]
rs4533897	0.82[JPT][hapmap]
rs62367607	0.87[ASN][1000 genomes]
rs62367633	0.96[ASN][1000 genomes]
rs62367649	0.98[ASN][1000 genomes]
rs62367650	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62367651	0.98[ASN][1000 genomes]
rs62367653	0.92[ASN][1000 genomes]
rs62368560	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62368561	0.98[ASN][1000 genomes]
rs62368564	0.98[ASN][1000 genomes]
rs62368566	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62368567	0.98[ASN][1000 genomes]
rs62368570	0.98[ASN][1000 genomes]
rs62368571	0.98[ASN][1000 genomes]
rs62368594	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6451697	0.86[YRI][hapmap]
rs6451699	0.86[YRI][hapmap]
rs6451705	0.84[YRI][hapmap]
rs6451719	0.94[ASN][1000 genomes]
rs6451720	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6862487	0.82[CHB][hapmap];0.82[JPT][hapmap];1.00[ASN][1000 genomes]
rs6863699	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6868763	0.94[ASN][1000 genomes]
rs6872959	0.83[EUR][1000 genomes]
rs6875118	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6878770	0.84[YRI][hapmap]
rs6885679	0.84[YRI][hapmap]
rs6893250	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6895327	0.84[YRI][hapmap]
rs6896693	0.84[YRI][hapmap]
rs6896932	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6898436	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71590644	0.94[ASN][1000 genomes]
rs71590645	0.94[ASN][1000 genomes]
rs71629182	0.94[ASN][1000 genomes]
rs71629184	0.98[ASN][1000 genomes]
rs71629185	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71629186	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71629187	0.98[ASN][1000 genomes]
rs7710628	0.84[YRI][hapmap]
rs7713458	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7713749	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7716562	0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs7718627	0.84[YRI][hapmap]
rs7736108	0.86[YRI][hapmap]
rs7737947	1.00[CEU][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16873438	NNT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 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	chr5:43610800-43649400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr5:43612600-43649400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr5:43620200-43650600	Weak transcription	Placenta	Placenta
10	chr5:43621200-43650200	Weak transcription	NHEK	skin
11	chr5:43621600-43651800	Weak transcription	HMEC	breast
12	chr5:43621800-43667400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr5:43624200-43649200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr5:43630200-43658800	Weak transcription	Stomach Mucosa	stomach
15	chr5:43631600-43649200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr5:43631600-43651400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr5:43631600-43664200	Weak transcription	A549	lung
18	chr5:43633000-43649200	Weak transcription	Ovary	ovary
19	chr5:43635000-43650000	Weak transcription	K562	blood
20	chr5:43635600-43649000	Weak transcription	Brain Germinal Matrix	brain
21	chr5:43635800-43649200	Weak transcription	Pancreas	Pancrea
22	chr5:43636400-43649600	Weak transcription	NHLF	lung
23	chr5:43636400-43664200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr5:43637800-43649200	Weak transcription	Aorta	Aorta
25	chr5:43637800-43649800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr5:43638200-43659200	Weak transcription	Colon Smooth Muscle	Colon
27	chr5:43639200-43665400	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr5:43640000-43665400	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr5:43642600-43649400	Weak transcription	Fetal Heart	heart
30	chr5:43642800-43649000	Weak transcription	Psoas Muscle	Psoas
31	chr5:43642800-43661200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr5:43642800-43665800	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr5:43643200-43652000	Strong transcription	Liver	Liver
34	chr5:43643200-43661000	Strong transcription	Duodenum Mucosa	Duodenum
35	chr5:43643200-43661400	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr5:43643200-43661600	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr5:43643400-43649200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr5:43643400-43665800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr5:43643600-43665200	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr5:43643800-43649200	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr5:43643800-43664600	Strong transcription	Dnd41	blood
42	chr5:43644200-43649200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr5:43644200-43649200	Weak transcription	Brain Angular Gyrus	brain
44	chr5:43644200-43649200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr5:43644200-43660600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr5:43644200-43664000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr5:43644600-43657400	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr5:43644600-43660000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr5:43644600-43661000	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr5:43644600-43661400	Strong transcription	Fetal Muscle Trunk	muscle

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