Variant report

Variant	rs62272243
Chromosome Location	chr3:160146522-160146523
allele	A/C
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	chr3:160143495-160147340	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr3:160146508-160147061	GM12892	blood:	n/a	n/a
3	POLR2A	chr3:160145522-160147054	K562	blood:	n/a	n/a
4	CEBPB	chr3:160146440-160146645	K562	blood:	n/a	n/a
5	POLR2A	chr3:160146522-160147041	K562	blood:	n/a	n/a
6	POLR2A	chr3:160145509-160146668	GM12892	blood:	n/a	n/a
7	POLR2A	chr3:160144960-160147335	K562	blood:	n/a	n/a
8	POLR2A	chr3:160145689-160147130	U87	brain:	n/a	n/a
9	POLR2A	chr3:160139039-160157396	K562	blood:	n/a	n/a
10	POLR2A	chr3:160146501-160147072	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr3:160144706-160147359	A549	lung:	n/a	n/a
12	POLR2A	chr3:160144524-160147375	GM12878	blood:	n/a	n/a
13	POLR2A	chr3:160146421-160146941	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr3:160146478-160146965	GM12892	blood:	n/a	n/a
15	POLR2A	chr3:160146433-160146904	PFSK-1	brain:	n/a	n/a
16	POLR2A	chr3:160146225-160146984	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
SMC4	TF binding region

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs2275153	0.84[AMR][1000 genomes]
rs2305401	0.84[AMR][1000 genomes]
rs2305406	0.84[AMR][1000 genomes]
rs33999879	0.84[AMR][1000 genomes]
rs3736627	0.84[AMR][1000 genomes]
rs41272959	0.84[AMR][1000 genomes]
rs57030267	0.84[AMR][1000 genomes]
rs57050097	0.84[AMR][1000 genomes]
rs57277659	0.84[AMR][1000 genomes]
rs57285344	0.84[AMR][1000 genomes]
rs57555307	0.84[AMR][1000 genomes]
rs58654032	0.84[AMR][1000 genomes]
rs58915028	0.84[AMR][1000 genomes]
rs59695030	0.84[AMR][1000 genomes]
rs59799252	0.84[AMR][1000 genomes]
rs60066272	0.84[AMR][1000 genomes]
rs60153357	0.84[AMR][1000 genomes]
rs60517889	0.84[AMR][1000 genomes]
rs60914777	0.84[AMR][1000 genomes]
rs61066536	0.84[AMR][1000 genomes]
rs62272168	1.00[AFR][1000 genomes]
rs62272171	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62272176	0.84[AMR][1000 genomes]
rs62272179	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs62272187	0.84[AMR][1000 genomes]
rs62272188	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs62272190	0.84[AMR][1000 genomes]
rs62272191	0.84[AMR][1000 genomes]
rs62272193	0.84[AMR][1000 genomes]
rs62272196	0.84[AMR][1000 genomes]
rs62272198	0.84[AMR][1000 genomes]
rs62272231	0.84[AMR][1000 genomes]
rs62272236	0.84[AMR][1000 genomes]
rs62272237	0.84[AMR][1000 genomes]
rs62272238	1.00[AFR][1000 genomes]
rs62272245	0.84[AMR][1000 genomes]
rs62272247	0.84[AMR][1000 genomes]
rs62272249	0.84[AMR][1000 genomes]
rs62272251	0.84[AMR][1000 genomes]
rs62272253	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62272254	0.84[AMR][1000 genomes]
rs62272255	0.84[AMR][1000 genomes]
rs62272256	0.84[AMR][1000 genomes]
rs62272257	0.84[AMR][1000 genomes]
rs62272258	0.84[AMR][1000 genomes]
rs62272259	0.84[AMR][1000 genomes]
rs62272781	0.84[AMR][1000 genomes]
rs62272783	0.84[AMR][1000 genomes]
rs62272785	0.84[AMR][1000 genomes]
rs62272787	0.84[AMR][1000 genomes]
rs62272788	0.84[AMR][1000 genomes]
rs62272790	0.84[AMR][1000 genomes]
rs62272793	0.84[AMR][1000 genomes]
rs62272799	0.84[AMR][1000 genomes]
rs66850724	0.84[AMR][1000 genomes]
rs73154564	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73154587	0.84[AMR][1000 genomes]
rs73155914	0.84[AMR][1000 genomes]
rs7648832	0.84[AMR][1000 genomes]
rs9637414	0.84[AMR][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	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	esv1800136	chr3:159950498-160278160	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	esv1801767	chr3:159950498-160279411	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
6	esv1801474	chr3:160012843-160153305	Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	206 gene(s)	inside rSNPs	diseases
7	nsv1008519	chr3:160038710-160292589	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	255 gene(s)	inside rSNPs	diseases
8	esv1795255	chr3:160089896-160153305	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	205 gene(s)	inside rSNPs	diseases
9	esv1801686	chr3:160089896-160248363	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	211 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160119800-160146600	Weak transcription	HSMMtube	muscle
2	chr3:160119800-160151800	Weak transcription	Brain Substantia Nigra	brain
3	chr3:160120200-160152400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr3:160120200-160164400	Weak transcription	Fetal Brain Male	brain
5	chr3:160121200-160157200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr3:160121200-160157400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:160121200-160157800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
8	chr3:160122000-160161000	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr3:160122000-160164400	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr3:160122000-160164600	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr3:160122200-160157400	Strong transcription	Fetal Thymus	thymus
12	chr3:160122600-160155000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:160122600-160156600	Strong transcription	K562	blood
14	chr3:160122800-160154200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr3:160123000-160153600	Weak transcription	Brain Anterior Caudate	brain
16	chr3:160123200-160155400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:160124000-160159000	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr3:160124200-160152600	Strong transcription	Hela-S3	cervix
19	chr3:160124600-160155000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:160125200-160159800	Strong transcription	HSMM	muscle
21	chr3:160127800-160154000	Strong transcription	HMEC	breast
22	chr3:160127800-160157000	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr3:160128000-160154200	Strong transcription	Dnd41	blood
24	chr3:160128200-160152400	Strong transcription	GM12878-XiMat	blood
25	chr3:160128400-160157200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:160128600-160158200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr3:160129400-160149200	Weak transcription	Brain Angular Gyrus	brain
28	chr3:160129600-160151400	Strong transcription	Osteobl	bone
29	chr3:160129600-160156600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:160129600-160157000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr3:160129800-160151600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:160130000-160155000	Strong transcription	Placenta	Placenta
33	chr3:160130000-160166200	Weak transcription	Colon Smooth Muscle	Colon
34	chr3:160130400-160154000	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr3:160130400-160157400	Strong transcription	NH-A	brain
36	chr3:160132000-160154200	Strong transcription	Duodenum Mucosa	Duodenum
37	chr3:160132000-160158800	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr3:160132200-160153200	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr3:160132200-160157000	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr3:160132400-160151600	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr3:160132400-160153200	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr3:160132400-160154200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr3:160132400-160154200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:160133600-160151400	Strong transcription	A549	lung
45	chr3:160133600-160152000	Weak transcription	Stomach Mucosa	stomach
46	chr3:160133800-160148600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr3:160133800-160164600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr3:160134400-160147600	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr3:160134600-160156800	Strong transcription	HUVEC	blood vessel
50	chr3:160134800-160158800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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