Variant report

Variant	rs73154596
Chromosome Location	chr3:160144863-160144864
allele	C/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	chr3:160144389-160145400	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr3:160143495-160147340	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr3:160144514-160145535	U87	brain:	n/a	n/a
4	POLR2A	chr3:160144490-160144903	MCF-7	breast:	n/a	n/a
5	POLR2A	chr3:160139039-160157396	K562	blood:	n/a	n/a
6	POLR2A	chr3:160144706-160147359	A549	lung:	n/a	n/a
7	POLR2A	chr3:160144524-160147375	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160143298..160145601-chr3:160163955..160166851,2	K562	blood:

Variant related genes	Relation type
SMC4	TF binding region
ENSG00000213186	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1141023	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17236389	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17236452	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17236487	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17826161	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1882124	0.84[ASN][1000 genomes]
rs1882128	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1920648	0.84[ASN][1000 genomes]
rs1920654	0.84[ASN][1000 genomes]
rs1979160	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2029361	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2152424	0.92[ASN][1000 genomes]
rs2272489	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35281166	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3737214	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41272955	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41272957	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4254702	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4434183	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4679883	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679887	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4679894	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4680577	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680582	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680590	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55853078	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55930449	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56030166	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56051094	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56322040	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6776582	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6780828	0.84[ASN][1000 genomes]
rs6806971	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73154549	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73154552	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154567	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73154591	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154600	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154602	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73155903	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73155920	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73155922	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73155924	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7622031	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9826290	0.92[ASN][1000 genomes]
rs9845172	0.84[ASN][1000 genomes]
rs9847144	0.84[ASN][1000 genomes]
rs9876980	0.84[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	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:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160119000-160145200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:160119800-160145200	Weak transcription	Brain Hippocampus Middle	brain
3	chr3:160119800-160146600	Weak transcription	HSMMtube	muscle
4	chr3:160119800-160151800	Weak transcription	Brain Substantia Nigra	brain
5	chr3:160120200-160152400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:160120200-160164400	Weak transcription	Fetal Brain Male	brain
7	chr3:160121200-160157200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr3:160121200-160157400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr3:160121200-160157800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr3:160122000-160161000	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr3:160122000-160164400	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr3:160122000-160164600	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr3:160122200-160157400	Strong transcription	Fetal Thymus	thymus
14	chr3:160122600-160155000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:160122600-160156600	Strong transcription	K562	blood
16	chr3:160122800-160154200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:160123000-160153600	Weak transcription	Brain Anterior Caudate	brain
18	chr3:160123200-160155400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:160124000-160159000	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr3:160124200-160152600	Strong transcription	Hela-S3	cervix
21	chr3:160124600-160155000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:160125200-160159800	Strong transcription	HSMM	muscle
23	chr3:160127800-160154000	Strong transcription	HMEC	breast
24	chr3:160127800-160157000	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr3:160128000-160154200	Strong transcription	Dnd41	blood
26	chr3:160128200-160152400	Strong transcription	GM12878-XiMat	blood
27	chr3:160128400-160157200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:160128600-160158200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:160129400-160149200	Weak transcription	Brain Angular Gyrus	brain
30	chr3:160129600-160151400	Strong transcription	Osteobl	bone
31	chr3:160129600-160156600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr3:160129600-160157000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr3:160129800-160151600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr3:160130000-160155000	Strong transcription	Placenta	Placenta
35	chr3:160130000-160166200	Weak transcription	Colon Smooth Muscle	Colon
36	chr3:160130400-160154000	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr3:160130400-160157400	Strong transcription	NH-A	brain
38	chr3:160132000-160154200	Strong transcription	Duodenum Mucosa	Duodenum
39	chr3:160132000-160158800	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr3:160132200-160145600	Strong transcription	HepG2	liver
41	chr3:160132200-160153200	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr3:160132200-160157000	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr3:160132400-160151600	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr3:160132400-160153200	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr3:160132400-160154200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr3:160132400-160154200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr3:160133600-160151400	Strong transcription	A549	lung
48	chr3:160133600-160152000	Weak transcription	Stomach Mucosa	stomach
49	chr3:160133800-160145200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:160133800-160148600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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