Variant report

Variant	rs3733839
Chromosome Location	chr5:43045271-43045272
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:43045132-43045415	K562	blood:	n/a	n/a
2	POLR2A	chr5:43044956-43046141	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr5:43045217-43046042	PANC-1	pancreas:	n/a	n/a
4	TCF7L2	chr5:43044414-43045616	PANC-1	pancreas:	n/a	n/a
5	TCF7L2	chr5:43045160-43045469	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr5:43044826-43045535	H1-neurons	neurons:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:43045206..43050609-chr5:43062079..43064977,5	K562	blood:
2	chr5:43014739..43026335-chr5:43034830..43045515,33	MCF-7	breast:
3	chr5:43034726..43053192-chr5:43061725..43074206,66	K562	blood:
4	chr5:43036901..43050217-chr5:43060442..43069391,53	MCF-7	breast:
5	chr5:43038662..43048059-chr5:43059399..43070773,40	MCF-7	breast:
6	chr5:43044445..43046601-chr5:43140326..43141953,2	MCF-7	breast:

No data

Variant related genes	Relation type
ANXA2R	TF binding region
ENSG00000272144	Chromatin interaction
ENSG00000177738	Chromatin interaction
ENSG00000172262	Chromatin interaction
ENSG00000251131	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10058374	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs10074873	0.94[JPT][hapmap]
rs10075647	0.80[CHB][hapmap];0.88[JPT][hapmap]
rs10078527	0.88[JPT][hapmap]
rs1032434	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10454865	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10805667	0.81[CHB][hapmap];0.93[JPT][hapmap]
rs10941607	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10941608	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11550285	0.92[ASN][1000 genomes]
rs11550286	0.93[ASN][1000 genomes]
rs11550287	0.90[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11740797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11742691	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11743246	0.80[ASN][1000 genomes]
rs11747015	0.83[AMR][1000 genomes]
rs11748187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11750239	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11949817	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11954543	0.80[ASN][1000 genomes]
rs11956243	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12109075	0.80[CHB][hapmap]
rs12188691	0.85[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13155513	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13159703	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13165504	0.82[ASN][1000 genomes]
rs13169563	0.98[ASN][1000 genomes]
rs13173064	0.92[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13665	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs1532331	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs17301375	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2452831	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316398	0.82[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs316405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316409	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316410	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316411	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs316418	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3207358	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34087147	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs34315422	0.95[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs34492794	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs34670023	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34808919	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34859360	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35085573	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs35541316	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35953019	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs36039989	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs36083302	0.95[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs3797312	0.80[ASN][1000 genomes]
rs3849698	0.90[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs3849699	0.85[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4498259	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs493097	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs504404	0.88[ASN][1000 genomes]
rs541143	0.94[JPT][hapmap]
rs55939188	0.85[AMR][1000 genomes]
rs56169202	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs581914	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62367685	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs62367688	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs62372869	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6414900	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs6451674	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs6451675	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs670206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6862639	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs6864223	0.93[ASN][1000 genomes]
rs6871636	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs6884303	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs6894506	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs7701510	0.82[CHB][hapmap]
rs7709181	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7729529	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7730004	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs9790935	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
2	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
3	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv534185	chr5:42804840-43067088	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	165 gene(s)	inside rSNPs	diseases
7	nsv1029288	chr5:42928085-43047323	Flanking Bivalent TSS/Enh Active TSS Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	120 gene(s)	inside rSNPs	diseases
8	nsv1024636	chr5:42959979-43295782	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
9	nsv537739	chr5:42959979-43295782	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3733839	ZNF131	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43043600-43050600	Weak transcription	GM12878-XiMat	blood
2	chr5:43043600-43052600	Weak transcription	A549	lung
3	chr5:43043600-43058200	Weak transcription	Gastric	stomach
4	chr5:43043600-43058200	Weak transcription	HSMMtube	muscle
5	chr5:43043600-43061600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:43043600-43063800	Weak transcription	Aorta	Aorta
7	chr5:43043600-43064000	Weak transcription	NHEK	skin
8	chr5:43043800-43045400	Bivalent Enhancer	Fetal Muscle Leg	muscle
9	chr5:43043800-43050600	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr5:43043800-43054400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr5:43043800-43057400	Weak transcription	Primary B cells from cord blood	blood
12	chr5:43043800-43058000	Weak transcription	HepG2	liver
13	chr5:43043800-43061200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr5:43043800-43064000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr5:43044200-43045400	Genic enhancers	Primary T cells fromperipheralblood	blood
16	chr5:43044200-43045400	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr5:43044200-43045800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
18	chr5:43044200-43046000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
19	chr5:43044400-43045400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr5:43044400-43045400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
21	chr5:43044400-43045400	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr5:43044400-43045400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr5:43044400-43045400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr5:43044400-43045400	Genic enhancers	Spleen	Spleen
25	chr5:43044400-43045600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr5:43044600-43045400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
27	chr5:43044600-43045400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr5:43044600-43045400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr5:43044600-43045800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
30	chr5:43044600-43052800	Weak transcription	Primary hematopoietic stem cells	blood
31	chr5:43044800-43045400	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
32	chr5:43044800-43045400	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
33	chr5:43044800-43045400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr5:43044800-43045400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr5:43044800-43045400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr5:43044800-43045400	Genic enhancers	Hela-S3	cervix
37	chr5:43044800-43045600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
38	chr5:43044800-43045600	Weak transcription	Small Intestine	intestine
39	chr5:43044800-43045800	Genic enhancers	Primary T cells from cord blood	blood
40	chr5:43044800-43045800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr5:43044800-43046000	Enhancers	Fetal Thymus	thymus
42	chr5:43044800-43046400	Weak transcription	Psoas Muscle	Psoas
43	chr5:43044800-43047000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr5:43044800-43047600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr5:43044800-43049000	Weak transcription	HSMM	muscle
46	chr5:43044800-43050600	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr5:43044800-43051200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr5:43044800-43052600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr5:43044800-43052600	Weak transcription	Placenta	Placenta
50	chr5:43044800-43058200	Weak transcription	Lung	lung

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