Variant report

Variant	rs13419000
Chromosome Location	chr2:153246147-153246148
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	POLR2A	chr2:153246138-153246356	A549	lung:	n/a	n/a
2	POLR2A	chr2:153246037-153246411	MCF-7	breast:	n/a	n/a
3	POLR2A	chr2:153246105-153246257	K562	blood:	n/a	n/a
4	POLR2A	chr2:153246100-153246305	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr2:153246118-153246245	ProgFib	skin:	n/a	n/a
6	POLR2A	chr2:153246019-153246439	MCF-7	breast:	n/a	n/a
7	POLR2A	chr2:153246138-153246274	GM12878	blood:	n/a	n/a
8	HEY1	chr2:153246096-153246312	K562	blood:	n/a	n/a
9	POLR2A	chr2:153246084-153246286	H1-hESC	embryonic stem cell:	n/a	n/a
10	E2F6	chr2:153246134-153246287	K562	blood:	n/a	n/a
11	MYC	chr2:153246069-153246318	MCF-7	breast:	n/a	n/a
12	POLR2A	chr2:153246073-153246358	GM12892	blood:	n/a	n/a
13	POLR2A	chr2:153246102-153246269	A549	lung:	n/a	n/a
14	POLR2A	chr2:153246122-153246287	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr2:153246058-153246219	HepG2	liver:	n/a	n/a
16	POLR2A	chr2:153246029-153246222	Hela-S3	cervix:	n/a	n/a
17	MYC	chr2:153246143-153246220	HUVEC	blood vessel:	n/a	n/a

Variant related genes	Relation type
ENSG00000213197	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10931069	0.83[JPT][hapmap]
rs13029771	0.83[JPT][hapmap]
rs13386403	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs13391023	0.82[CEU][hapmap];0.80[CHB][hapmap];0.92[JPT][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13396439	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13397890	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13402243	0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13405110	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13405868	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13414887	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13418748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13419948	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13427076	0.82[CEU][hapmap]
rs13428569	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs13430448	0.91[CEU][hapmap];0.85[JPT][hapmap];0.89[EUR][1000 genomes]
rs16831028	0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs2345873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3811577	0.91[CEU][hapmap];0.92[JPT][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3890370	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4425036	0.90[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes]
rs56095564	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58092541	0.82[AMR][1000 genomes]
rs61292193	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62180761	0.82[AMR][1000 genomes]
rs62180766	0.94[ASN][1000 genomes]
rs6715843	0.83[JPT][hapmap]
rs6725656	0.83[JPT][hapmap]
rs6725789	0.81[JPT][hapmap]
rs6754501	0.83[JPT][hapmap]
rs6761815	0.91[CEU][hapmap];0.92[JPT][hapmap];0.89[EUR][1000 genomes]
rs73967855	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73967856	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73967858	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73967990	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[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	nsv834419	chr2:153179420-153381476	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1005012	chr2:153206764-153273886	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	esv3693436	chr2:153219836-153479857	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153207600-153246400	Weak transcription	Fetal Intestine Small	intestine
2	chr2:153226200-153249400	Weak transcription	Right Ventricle	heart
3	chr2:153226200-153251800	Weak transcription	HSMMtube	muscle
4	chr2:153229200-153252400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr2:153233400-153249000	Weak transcription	Gastric	stomach
6	chr2:153233600-153246200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:153233800-153255400	Weak transcription	NHEK	skin
8	chr2:153237400-153246200	Weak transcription	Placenta	Placenta
9	chr2:153237400-153249000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:153237400-153255400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:153237400-153255400	Weak transcription	HMEC	breast
12	chr2:153238400-153246400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr2:153238600-153246600	Weak transcription	Ovary	ovary
14	chr2:153238600-153258600	Weak transcription	Left Ventricle	heart
15	chr2:153241200-153251600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr2:153241200-153255400	Weak transcription	Pancreas	Pancrea
17	chr2:153241600-153249000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr2:153242600-153247200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr2:153242800-153247800	Weak transcription	Psoas Muscle	Psoas
20	chr2:153242800-153248000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr2:153242800-153248000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:153242800-153249200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:153242800-153252600	Weak transcription	A549	lung
24	chr2:153243000-153247200	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr2:153243000-153251600	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr2:153243200-153249200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr2:153243400-153247400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr2:153243400-153252600	Weak transcription	Fetal Brain Female	brain
29	chr2:153243600-153247000	Weak transcription	Brain Anterior Caudate	brain
30	chr2:153243800-153246800	Weak transcription	Stomach Mucosa	stomach
31	chr2:153243800-153252000	Weak transcription	Fetal Lung	lung
32	chr2:153244400-153247200	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr2:153244600-153246800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:153245000-153246200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:153245000-153247000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr2:153245000-153249200	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr2:153245000-153251800	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr2:153245400-153246600	Weak transcription	Brain Substantia Nigra	brain
39	chr2:153245600-153246400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr2:153245600-153247000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr2:153245800-153247000	Weak transcription	Brain Hippocampus Middle	brain
42	chr2:153245800-153247200	Weak transcription	Brain Cingulate Gyrus	brain
43	chr2:153245800-153247400	Weak transcription	Brain Angular Gyrus	brain
44	chr2:153245800-153250800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr2:153245800-153250800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr2:153246000-153246400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr2:153246000-153247000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr2:153246000-153247200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr2:153246000-153247400	Strong transcription	Fetal Stomach	stomach
50	chr2:153246000-153248200	Strong transcription	HepG2	liver

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