Variant report

Variant	rs13028500
Chromosome Location	chr2:99528296-99528297
allele	A/G
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	MYC	chr2:99528245-99529636	MCF10A-Er-Src	breast:	n/a	chr2:99528453-99528462 chr2:99529096-99529106
2	RUNX3	chr2:99528204-99528468	GM12878	blood:	n/a	chr2:99528276-99528293 chr2:99528367-99528382 chr2:99528338-99528353
3	STAT3	chr2:99528169-99530733	MCF10A-Er-Src	breast:	n/a	chr2:99529112-99529124 chr2:99530591-99530599 chr2:99529108-99529120
4	STAT3	chr2:99528211-99528688	MCF10A-Er-Src	breast:	n/a	n/a
5	MYC	chr2:99528209-99530685	MCF10A-Er-Src	breast:	n/a	chr2:99528453-99528462 chr2:99529096-99529106
6	POLR2A	chr2:99528248-99528326	MCF10A-Er-Src	breast:	n/a	n/a
7	EP300	chr2:99528238-99528441	GM12878	blood:	n/a	n/a
8	BHLHE40	chr2:99528258-99528463	GM12878	blood:	n/a	n/a
9	EP300	chr2:99528253-99528551	GM12878	blood:	n/a	n/a
10	NR3C1	chr2:99528053-99529396	A549	lung:	n/a	chr2:99528062-99528080 chr2:99528350-99528366 chr2:99528064-99528078 chr2:99528727-99528736 chr2:99529201-99529210 chr2:99528350-99528366 chr2:99528350-99528366 chr2:99529090-99529103
11	NR3C1	chr2:99528117-99528677	A549	lung:	n/a	chr2:99528350-99528366 chr2:99528350-99528366 chr2:99528350-99528366
12	RUNX3	chr2:99528185-99528415	GM12878	blood:	n/a	chr2:99528276-99528293 chr2:99528367-99528382 chr2:99528338-99528353
13	FOS	chr2:99528273-99528641	HUVEC	blood vessel:	n/a	chr2:99528452-99528462 chr2:99528453-99528461 chr2:99528451-99528463 chr2:99528452-99528462 chr2:99528451-99528462
14	NR3C1	chr2:99528177-99528615	A549	lung:	n/a	chr2:99528350-99528366 chr2:99528350-99528366 chr2:99528350-99528366
15	FOS	chr2:99528226-99529464	MCF10A-Er-Src	breast:	n/a	chr2:99529444-99529458 chr2:99529200-99529212 chr2:99528452-99528462 chr2:99528453-99528461 chr2:99529200-99529211 chr2:99528451-99528463 chr2:99529202-99529210 chr2:99528452-99528462 chr2:99528451-99528462
16	MAFK	chr2:99528286-99528465	IMR90	lung:	n/a	n/a
17	NR3C1	chr2:99527999-99529464	A549	lung:	n/a	chr2:99528062-99528080 chr2:99528350-99528366 chr2:99528064-99528078 chr2:99528727-99528736 chr2:99529201-99529210 chr2:99528350-99528366 chr2:99528350-99528366 chr2:99529090-99529103
18	FOS	chr2:99528225-99529678	MCF10A-Er-Src	breast:	n/a	chr2:99529444-99529458 chr2:99529200-99529212 chr2:99528452-99528462 chr2:99528453-99528461 chr2:99529200-99529211 chr2:99528451-99528463 chr2:99529202-99529210 chr2:99528452-99528462 chr2:99528451-99528462
19	FOS	chr2:99528203-99528718	MCF10A-Er-Src	breast:	n/a	chr2:99528452-99528462 chr2:99528453-99528461 chr2:99528451-99528463 chr2:99528452-99528462 chr2:99528451-99528462
20	EBF1	chr2:99528204-99528599	GM12878	blood:	n/a	chr2:99528381-99528392
21	JUND	chr2:99528160-99529585	SK-N-SH	brain:	n/a	chr2:99529444-99529458 chr2:99529200-99529212 chr2:99528452-99528462 chr2:99528453-99528461 chr2:99528451-99528463 chr2:99529202-99529210 chr2:99528452-99528462
22	STAT3	chr2:99528145-99528518	MCF10A-Er-Src	breast:	n/a	n/a
23	STAT3	chr2:99528165-99528574	MCF10A-Er-Src	breast:	n/a	n/a
24	NR3C1	chr2:99528217-99528402	A549	lung:	n/a	chr2:99528350-99528366 chr2:99528350-99528366 chr2:99528350-99528366
25	NR3C1	chr2:99528202-99528589	A549	lung:	n/a	chr2:99528350-99528366 chr2:99528350-99528366 chr2:99528350-99528366

No.	Distal block	Cell Line	Cell type
1	chr2:99484412..99487919-chr2:99523957..99528531,6	MCF-7	breast:
2	chr2:99525536..99528520-chr2:99541090..99543085,2	MCF-7	breast:
3	chr2:99523325..99526612-chr2:99528163..99531065,4	K562	blood:

Variant related genes	Relation type
KIAA1211L	TF binding region
ENSG00000196872	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10172158	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10192266	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11123755	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12468024	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12474283	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12712038	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12712041	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12712042	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12712043	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13004700	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs13005124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13006398	0.80[EUR][1000 genomes]
rs13011428	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13024838	0.85[EUR][1000 genomes]
rs13025076	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13025913	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1581251	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1607256	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17758170	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs1878589	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs1949424	0.83[EUR][1000 genomes]
rs1976766	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2048949	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4311103	0.88[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4850889	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4850890	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4851167	0.83[AMR][1000 genomes]
rs4851170	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4851171	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4851173	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4851174	0.95[CEU][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4851175	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4851176	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4851177	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs56125264	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6419564	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6542841	0.92[CEU][hapmap]
rs6542843	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6542845	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6714243	0.83[AMR][1000 genomes]
rs6717372	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6724477	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6739176	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6739503	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6741166	0.85[EUR][1000 genomes]
rs6742047	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6752025	0.83[EUR][1000 genomes]
rs6757098	0.91[CEU][hapmap]
rs6760065	0.91[CEU][hapmap]
rs7423519	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs7565819	0.85[EUR][1000 genomes]
rs7588441	0.85[EUR][1000 genomes]
rs7593332	0.83[EUR][1000 genomes]
rs7608889	0.91[CHB][hapmap];0.82[AMR][1000 genomes]
rs883773	0.92[CEU][hapmap]
rs908672	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs925887	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[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	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv582518	chr2:99498774-99546355	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv874697	chr2:99520608-99558970	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13028500	TSGA10	cis	Lymphoblastoid	GTEx
rs13028500	LIPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99520800-99528600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr2:99523800-99530000	Enhancers	Fetal Muscle Leg	muscle
3	chr2:99524400-99528400	Enhancers	HMEC	breast
4	chr2:99524400-99534400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:99524600-99532400	Enhancers	Pancreas	Pancrea
6	chr2:99525200-99530600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr2:99525800-99529600	Weak transcription	Brain Angular Gyrus	brain
8	chr2:99526000-99530400	Enhancers	Brain Anterior Caudate	brain
9	chr2:99526000-99530800	Enhancers	Spleen	Spleen
10	chr2:99526400-99528400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:99526400-99528600	Weak transcription	Brain Hippocampus Middle	brain
12	chr2:99526400-99528800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr2:99526400-99528800	Weak transcription	Right Ventricle	heart
14	chr2:99526400-99529000	Enhancers	Fetal Intestine Large	intestine
15	chr2:99526400-99530200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr2:99526400-99534200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:99526600-99528400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:99526600-99528400	Weak transcription	Fetal Brain Male	brain
19	chr2:99526600-99528400	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr2:99526600-99528400	Weak transcription	Stomach Mucosa	stomach
21	chr2:99526600-99528600	Weak transcription	Brain Germinal Matrix	brain
22	chr2:99526600-99528600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr2:99526600-99528600	Weak transcription	Fetal Brain Female	brain
24	chr2:99526600-99528800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:99526600-99528800	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr2:99526600-99528800	Weak transcription	Fetal Heart	heart
27	chr2:99526600-99528800	Weak transcription	Lung	lung
28	chr2:99526600-99528800	Weak transcription	Ovary	ovary
29	chr2:99526600-99529000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr2:99526600-99529800	Enhancers	HUVEC	blood vessel
31	chr2:99526600-99530400	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr2:99526600-99530400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr2:99526600-99533400	Weak transcription	Left Ventricle	heart
34	chr2:99526800-99529600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr2:99527200-99530200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr2:99527200-99530800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
37	chr2:99527200-99531000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr2:99527200-99532000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
39	chr2:99527200-99533600	Enhancers	Esophagus	oesophagus
40	chr2:99527400-99528600	Enhancers	Muscle Satellite Cultured Cells	--
41	chr2:99527400-99528600	Enhancers	HSMM	muscle
42	chr2:99527400-99528800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr2:99527600-99528600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr2:99527600-99528600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr2:99527600-99528600	Enhancers	NH-A	brain
46	chr2:99527600-99530200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
47	chr2:99527600-99531400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr2:99527800-99528400	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr2:99527800-99529000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr2:99527800-99529200	Enhancers	Fetal Lung	lung

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