Variant report

Variant	rs6863360
Chromosome Location	chr5:43298515-43298516
allele	C/T
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	chr5:43298405-43299082	SH-SY5Y	brain:	n/a	n/a
2	TCF12	chr5:43298483-43298898	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr5:43297959-43299477	K562	blood:	n/a	n/a
4	GATA2	chr5:43298515-43299086	SH-SY5Y	brain:	n/a	n/a
5	POLR2A	chr5:43297999-43299179	HepG2	liver:	n/a	n/a
6	POLR2A	chr5:43298022-43299178	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:43296533..43300928-chr5:43302565..43304605,4	K562	blood:
2	chr5:43296533..43300517-chr5:43302565..43304936,4	K562	blood:
3	chr5:43293726..43296499-chr5:43296794..43299254,2	MCF-7	breast:

Variant related genes	Relation type
HMGCS1	TF binding region
ENSG00000112972	Chromatin interaction

Extended variants
information (count: 150 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10039048	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10039617	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10512825	0.92[EUR][1000 genomes]
rs10512827	0.83[EUR][1000 genomes]
rs10512828	0.83[EUR][1000 genomes]
rs10805671	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10805672	0.92[EUR][1000 genomes]
rs10805673	0.86[EUR][1000 genomes]
rs10805674	0.85[EUR][1000 genomes]
rs10805675	0.83[EUR][1000 genomes]
rs10941620	0.83[EUR][1000 genomes]
rs10941621	0.92[EUR][1000 genomes]
rs10941622	0.92[EUR][1000 genomes]
rs10941623	0.92[EUR][1000 genomes]
rs10941628	0.89[EUR][1000 genomes]
rs10941630	0.86[EUR][1000 genomes]
rs10941631	0.83[EUR][1000 genomes]
rs10941632	0.82[EUR][1000 genomes]
rs11738086	0.86[EUR][1000 genomes]
rs11739009	0.90[EUR][1000 genomes]
rs11739665	0.92[EUR][1000 genomes]
rs11740128	0.83[EUR][1000 genomes]
rs11741246	0.89[EUR][1000 genomes]
rs11742171	0.86[EUR][1000 genomes]
rs11742712	0.90[EUR][1000 genomes]
rs11743622	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11743633	0.81[EUR][1000 genomes]
rs11746629	0.83[EUR][1000 genomes]
rs11747105	0.89[EUR][1000 genomes]
rs11747834	0.89[EUR][1000 genomes]
rs11950040	0.80[EUR][1000 genomes]
rs11950448	0.86[EUR][1000 genomes]
rs11951584	0.86[EUR][1000 genomes]
rs11956635	0.82[EUR][1000 genomes]
rs11956936	0.83[EUR][1000 genomes]
rs11956988	0.84[EUR][1000 genomes]
rs11960415	0.82[EUR][1000 genomes]
rs12109933	0.83[EUR][1000 genomes]
rs12189016	0.89[EUR][1000 genomes]
rs12189447	0.86[EUR][1000 genomes]
rs12513864	0.80[EUR][1000 genomes]
rs12514393	0.90[EUR][1000 genomes]
rs12514399	0.91[EUR][1000 genomes]
rs12515072	0.92[EUR][1000 genomes]
rs12516435	0.84[EUR][1000 genomes]
rs12517362	0.84[EUR][1000 genomes]
rs12518032	0.92[EUR][1000 genomes]
rs12518127	0.83[EUR][1000 genomes]
rs12519554	0.83[EUR][1000 genomes]
rs12520012	0.92[EUR][1000 genomes]
rs12520895	0.82[EUR][1000 genomes]
rs12522178	0.89[EUR][1000 genomes]
rs13161494	0.86[ASN][1000 genomes]
rs13187876	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13659	0.91[EUR][1000 genomes]
rs1545753	0.91[EUR][1000 genomes]
rs1548097	0.92[EUR][1000 genomes]
rs1564196	0.86[EUR][1000 genomes]
rs1564197	0.86[EUR][1000 genomes]
rs1564198	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2086133	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2126947	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2126948	0.90[EUR][1000 genomes]
rs2126949	0.90[EUR][1000 genomes]
rs2169781	0.89[EUR][1000 genomes]
rs2330150	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2330242	0.83[EUR][1000 genomes]
rs2330243	0.86[ASN][1000 genomes]
rs35231094	0.83[EUR][1000 genomes]
rs35239179	0.92[EUR][1000 genomes]
rs3733768	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733769	0.92[EUR][1000 genomes]
rs4050485	0.86[EUR][1000 genomes]
rs4254917	0.82[AMR][1000 genomes]
rs4288122	0.86[EUR][1000 genomes]
rs4320264	0.86[EUR][1000 genomes]
rs4373285	0.92[EUR][1000 genomes]
rs4395639	0.88[EUR][1000 genomes]
rs4443425	0.85[EUR][1000 genomes]
rs4443426	0.82[EUR][1000 genomes]
rs4574553	0.86[EUR][1000 genomes]
rs4591755	0.89[EUR][1000 genomes]
rs4866734	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4866737	0.90[EUR][1000 genomes]
rs4866738	0.90[EUR][1000 genomes]
rs4866741	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4866813	0.92[EUR][1000 genomes]
rs4866820	0.91[EUR][1000 genomes]
rs4866821	0.85[EUR][1000 genomes]
rs4866822	0.86[EUR][1000 genomes]
rs4866824	0.86[EUR][1000 genomes]
rs4866825	0.85[EUR][1000 genomes]
rs4866826	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55634155	0.89[EUR][1000 genomes]
rs55647314	0.86[EUR][1000 genomes]
rs55759097	0.80[EUR][1000 genomes]
rs55759722	0.84[EUR][1000 genomes]
rs55794239	0.91[EUR][1000 genomes]
rs55800451	0.87[EUR][1000 genomes]
rs55992392	0.85[EUR][1000 genomes]
rs56023994	0.86[EUR][1000 genomes]
rs56029402	0.88[EUR][1000 genomes]
rs56071328	0.85[EUR][1000 genomes]
rs56114604	0.92[EUR][1000 genomes]
rs56185290	0.85[EUR][1000 genomes]
rs56206275	0.86[EUR][1000 genomes]
rs57066570	0.85[EUR][1000 genomes]
rs57392430	0.88[EUR][1000 genomes]
rs57401732	0.90[EUR][1000 genomes]
rs58358642	0.85[EUR][1000 genomes]
rs58679159	0.90[EUR][1000 genomes]
rs58966636	0.85[EUR][1000 genomes]
rs59078439	0.86[EUR][1000 genomes]
rs59625262	0.85[EUR][1000 genomes]
rs59814709	0.86[EUR][1000 genomes]
rs60207549	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60445501	0.90[EUR][1000 genomes]
rs61627503	0.84[EUR][1000 genomes]
rs6451684	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66585077	0.83[EUR][1000 genomes]
rs66691321	0.92[EUR][1000 genomes]
rs66914803	0.90[EUR][1000 genomes]
rs67415672	0.87[EUR][1000 genomes]
rs67497876	0.89[EUR][1000 genomes]
rs67620667	0.83[EUR][1000 genomes]
rs67651757	0.89[EUR][1000 genomes]
rs67817333	0.91[EUR][1000 genomes]
rs6814	0.91[EUR][1000 genomes]
rs6863246	0.86[EUR][1000 genomes]
rs6867954	0.82[EUR][1000 genomes]
rs6886499	0.83[EUR][1000 genomes]
rs6887351	0.86[EUR][1000 genomes]
rs6895805	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6898398	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7445066	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7701391	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7704588	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7708779	0.86[EUR][1000 genomes]
rs7714027	0.81[EUR][1000 genomes]
rs7714919	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7716091	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7720165	0.92[EUR][1000 genomes]
rs7722781	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7734293	0.83[EUR][1000 genomes]
rs9292871	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9292874	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9790987	0.92[EUR][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	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
2	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
3	nsv508352	chr5:43237830-43391062	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6863360	NNT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43284200-43309400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:43285000-43300800	Strong transcription	Cortex derived primary cultured neurospheres	brain
3	chr5:43285600-43300000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr5:43285600-43302000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr5:43285600-43302800	Strong transcription	Duodenum Mucosa	Duodenum
6	chr5:43286200-43300600	Strong transcription	Fetal Intestine Large	intestine
7	chr5:43286400-43302200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr5:43286400-43302400	Strong transcription	GM12878-XiMat	blood
9	chr5:43286600-43300400	Strong transcription	Fetal Thymus	thymus
10	chr5:43286600-43300800	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr5:43286600-43301000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr5:43286600-43301400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr5:43286600-43303000	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr5:43286600-43303000	Strong transcription	Primary hematopoietic stem cells	blood
15	chr5:43286800-43300000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr5:43286800-43300400	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr5:43286800-43300400	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr5:43286800-43301000	Strong transcription	K562	blood
19	chr5:43286800-43301400	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr5:43286800-43301800	Strong transcription	HMEC	breast
21	chr5:43286800-43302400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr5:43286800-43302600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr5:43286800-43302600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr5:43286800-43304400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr5:43287000-43302800	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr5:43287000-43305000	Strong transcription	HUVEC	blood vessel
27	chr5:43287200-43301000	Strong transcription	Primary B cells from peripheral blood	blood
28	chr5:43287400-43298600	Weak transcription	Right Ventricle	heart
29	chr5:43287400-43300800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr5:43287400-43302600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr5:43287400-43302800	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr5:43287600-43302000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr5:43287800-43298800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr5:43287800-43299400	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr5:43287800-43300600	Strong transcription	HepG2	liver
36	chr5:43287800-43303600	Strong transcription	H9 Cell Line	embryonic stem cell
37	chr5:43288200-43312400	Weak transcription	Spleen	Spleen
38	chr5:43288600-43310000	Weak transcription	Aorta	Aorta
39	chr5:43288800-43303600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr5:43289600-43303800	Strong transcription	Primary B cells from cord blood	blood
41	chr5:43289800-43300800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr5:43290200-43298800	Strong transcription	Colon Smooth Muscle	Colon
43	chr5:43290400-43298800	Strong transcription	Brain Germinal Matrix	brain
44	chr5:43290400-43299200	Strong transcription	Fetal Brain Female	brain
45	chr5:43290400-43299200	Strong transcription	Fetal Lung	lung
46	chr5:43290400-43302400	Strong transcription	Primary T cells from cord blood	blood
47	chr5:43290600-43298800	Strong transcription	Brain Anterior Caudate	brain
48	chr5:43290600-43298800	Strong transcription	Brain Cingulate Gyrus	brain
49	chr5:43290600-43299400	Strong transcription	Placenta	Placenta
50	chr5:43290600-43299400	Strong transcription	HSMM	muscle

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