Variant report

Variant	rs13401578
Chromosome Location	chr2:233671539-233671540
allele	G/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	POLR2A	chr2:233671531-233671539	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
GIGYF2	TF binding region

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10176930	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10190211	0.90[ASN][1000 genomes]
rs10207739	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10933407	0.90[ASN][1000 genomes]
rs10933408	0.90[ASN][1000 genomes]
rs11679581	0.86[ASN][1000 genomes]
rs11684636	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11685169	0.90[ASN][1000 genomes]
rs11688622	0.86[ASN][1000 genomes]
rs11688691	0.86[ASN][1000 genomes]
rs11689661	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11694434	0.94[ASN][1000 genomes]
rs11695762	0.98[ASN][1000 genomes]
rs11904619	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12052869	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12328140	0.81[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs12694915	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.86[ASN][1000 genomes]
rs12694916	0.90[ASN][1000 genomes]
rs12988087	0.86[ASN][1000 genomes]
rs13035517	1.00[CHB][hapmap]
rs13383733	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13386650	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs13387762	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13390935	0.89[CHB][hapmap]
rs13408229	0.85[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13412034	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs13412513	0.90[ASN][1000 genomes]
rs13424896	0.86[CHB][hapmap]
rs13425525	0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs13425918	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13429857	0.86[ASN][1000 genomes]
rs1446307	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs2289914	0.82[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2289915	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2292724	1.00[CHB][hapmap]
rs2292725	1.00[CHB][hapmap]
rs2293782	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2305139	0.94[ASN][1000 genomes]
rs34063802	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs34832091	0.90[ASN][1000 genomes]
rs35778045	0.94[ASN][1000 genomes]
rs35785837	0.90[ASN][1000 genomes]
rs35928329	0.90[ASN][1000 genomes]
rs41266951	0.94[ASN][1000 genomes]
rs56054779	0.94[ASN][1000 genomes]
rs62193305	0.90[ASN][1000 genomes]
rs6747479	0.83[AFR][1000 genomes]
rs73005582	0.86[ASN][1000 genomes]
rs7557131	0.86[ASN][1000 genomes]
rs7564554	0.82[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs9288675	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9288676	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9808146	0.98[ASN][1000 genomes]
rs9973586	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948470	chr2:233166262-233886732	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1005123	chr2:233227729-233920152	Enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv536173	chr2:233227729-233920152	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv834570	chr2:233639160-233805067	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv460134	chr2:233639909-233714686	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv584696	chr2:233639909-233714686	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	esv3427756	chr2:233661496-233680721	Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233649000-233680600	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr2:233655600-233689200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:233656800-233674000	Weak transcription	Fetal Heart	heart
4	chr2:233659600-233671600	Weak transcription	Spleen	Spleen
5	chr2:233659800-233672400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr2:233660800-233688600	Weak transcription	Psoas Muscle	Psoas
7	chr2:233662400-233672400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr2:233662400-233672600	Weak transcription	K562	blood
9	chr2:233662600-233679800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:233665000-233672200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr2:233665000-233692600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr2:233665400-233685800	Strong transcription	Fetal Lung	lung
13	chr2:233665800-233734200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr2:233666200-233671600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr2:233666600-233680000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr2:233667600-233726400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:233667800-233671600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:233667800-233693400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr2:233668000-233673400	Strong transcription	Primary hematopoietic stem cells	blood
20	chr2:233669000-233701800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr2:233669200-233682600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr2:233669200-233690400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr2:233669400-233672000	Strong transcription	Primary B cells from cord blood	blood
24	chr2:233669400-233678400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr2:233669400-233690400	Strong transcription	Dnd41	blood
26	chr2:233669400-233703600	Strong transcription	Liver	Liver
27	chr2:233669600-233682400	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr2:233669600-233686200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr2:233669600-233690400	Strong transcription	Placenta	Placenta
30	chr2:233669600-233690800	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr2:233669800-233681000	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr2:233669800-233686200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:233669800-233686400	Strong transcription	Primary B cells from peripheral blood	blood
34	chr2:233669800-233692000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr2:233670000-233672400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr2:233670000-233678400	Strong transcription	HSMM	muscle
37	chr2:233670000-233679400	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr2:233670000-233686200	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr2:233670000-233690800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr2:233670000-233701600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr2:233670200-233671800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
42	chr2:233670200-233678400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr2:233670200-233682400	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr2:233670200-233683200	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr2:233670200-233684000	Strong transcription	GM12878-XiMat	blood
46	chr2:233670200-233688800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr2:233670200-233692200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr2:233670200-233699600	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr2:233670200-233702600	Strong transcription	HepG2	liver
50	chr2:233670600-233677400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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