Variant report

Variant	rs55855322
Chromosome Location	chr5:43519785-43519786
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:43519498-43519959	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:43483515..43485474-chr5:43518354..43520357,2	MCF-7	breast:
2	chr5:43517204..43520690-chr5:43533349..43537040,3	K562	blood:
3	chr5:43513317..43519979-chr5:43552519..43558793,19	K562	blood:
4	chr5:43512267..43517273-chr5:43518351..43521279,8	K562	blood:
5	chr5:43120558..43123353-chr5:43518356..43521146,2	K562	blood:
6	chr5:43519158..43521052-chr5:43546344..43548827,3	K562	blood:
7	chr5:43514344..43517074-chr5:43518051..43519887,3	K562	blood:

No data

Variant related genes	Relation type
C5orf34	TF binding region
ENSG00000172244	Chromatin interaction
ENSG00000248240	Chromatin interaction
ENSG00000151881	Chromatin interaction
ENSG00000172239	Chromatin interaction
ENSG00000172262	Chromatin interaction
ENSG00000249492	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10036954	0.92[ASN][1000 genomes]
rs10038545	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10053229	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10054519	0.91[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs10059912	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10059993	0.83[ASN][1000 genomes]
rs10065689	0.83[ASN][1000 genomes]
rs10066408	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10068064	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10462051	0.96[ASN][1000 genomes]
rs10472380	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs10473310	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs10473311	0.81[ASN][1000 genomes]
rs11949083	0.86[ASN][1000 genomes]
rs11958046	0.86[ASN][1000 genomes]
rs11959811	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12332560	0.96[ASN][1000 genomes]
rs12521249	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12651879	0.94[ASN][1000 genomes]
rs12697457	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13189484	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13359906	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13360902	0.84[EUR][1000 genomes]
rs1366410	0.81[ASN][1000 genomes]
rs1389870	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2131998	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2132001	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2132003	0.97[AFR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28437972	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28606458	0.82[ASN][1000 genomes]
rs3776423	0.92[ASN][1000 genomes]
rs4072918	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4072919	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4074777	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4331909	1.00[ASN][1000 genomes]
rs4386738	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4428418	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4467713	1.00[ASN][1000 genomes]
rs4535459	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4610465	0.81[EUR][1000 genomes]
rs4866833	1.00[ASN][1000 genomes]
rs4866835	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55667604	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56008952	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56097465	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56252541	0.82[ASN][1000 genomes]
rs56333629	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57403343	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59001943	1.00[ASN][1000 genomes]
rs59224335	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60297702	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6451697	0.91[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6451699	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6451704	0.84[ASN][1000 genomes]
rs6451705	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6451712	1.00[ASN][1000 genomes]
rs66495712	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67466542	0.92[ASN][1000 genomes]
rs67581152	0.94[ASN][1000 genomes]
rs6858942	0.80[ASN][1000 genomes]
rs6860493	0.84[ASN][1000 genomes]
rs6866325	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6866802	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6869933	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6878770	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6884661	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6885679	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6891363	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6895327	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6896693	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6898866	0.86[ASN][1000 genomes]
rs72756535	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72758674	0.84[ASN][1000 genomes]
rs750583	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7705166	0.86[ASN][1000 genomes]
rs7706431	0.86[ASN][1000 genomes]
rs7710628	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7713479	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7715782	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7717636	0.96[ASN][1000 genomes]
rs7718627	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7732140	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7732656	0.84[ASN][1000 genomes]
rs7734393	0.83[ASN][1000 genomes]
rs7736108	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7736615	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7737793	0.86[EUR][1000 genomes]
rs9687341	0.94[ASN][1000 genomes]
rs9885189	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[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	esv1835057	chr5:43515280-43557405	Active TSS Flanking Active TSS Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
4	esv1835614	chr5:43515280-43561759	Genic enhancers Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
5	esv1837000	chr5:43515280-43561759	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs55855322	NNT	cis	multi-tissue	Pritchard
rs55855322	NNT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43515400-43523800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:43515400-43524000	Weak transcription	Spleen	Spleen
3	chr5:43515600-43523400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:43515600-43523800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr5:43515600-43523800	Weak transcription	Gastric	stomach
6	chr5:43515600-43533800	Weak transcription	Small Intestine	intestine
7	chr5:43515600-43534000	Weak transcription	Esophagus	oesophagus
8	chr5:43515800-43523400	Weak transcription	Lung	lung
9	chr5:43515800-43523800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr5:43515800-43523800	Weak transcription	Ovary	ovary
11	chr5:43515800-43525400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr5:43515800-43525600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr5:43516000-43523200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr5:43516000-43523200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr5:43516000-43523200	Weak transcription	Fetal Muscle Trunk	muscle
16	chr5:43516000-43523200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr5:43516000-43523400	Weak transcription	Primary T cells from cord blood	blood
18	chr5:43516000-43523400	Weak transcription	Fetal Brain Female	brain
19	chr5:43516000-43523400	Weak transcription	Left Ventricle	heart
20	chr5:43516000-43523400	Weak transcription	Psoas Muscle	Psoas
21	chr5:43516000-43523400	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr5:43516000-43523800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr5:43516000-43523800	Weak transcription	Brain Germinal Matrix	brain
24	chr5:43516000-43523800	Weak transcription	Right Ventricle	heart
25	chr5:43516000-43524000	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr5:43516000-43524000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr5:43516000-43524000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr5:43516000-43524000	Weak transcription	Aorta	Aorta
29	chr5:43516000-43525000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr5:43516000-43525200	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr5:43516000-43525200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr5:43516000-43525200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr5:43516000-43525200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr5:43516000-43525200	Weak transcription	Fetal Brain Male	brain
35	chr5:43516000-43525400	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr5:43516000-43525400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr5:43516000-43525400	Weak transcription	Rectal Smooth Muscle	rectum
38	chr5:43516000-43525600	Weak transcription	NHDF-Ad	bronchial
39	chr5:43516000-43527400	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr5:43516000-43528000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr5:43516000-43528200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr5:43516000-43529400	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr5:43516000-43533800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr5:43516000-43534000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr5:43516200-43523200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr5:43516200-43523200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr5:43516200-43523200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr5:43516200-43523200	Weak transcription	Primary B cells from cord blood	blood
49	chr5:43516200-43523200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr5:43516200-43523200	Weak transcription	Placenta	Placenta

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