Variant report

Variant	rs6781020
Chromosome Location	chr3:160134954-160134955
allele	A/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	chr3:160134931-160135305	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:160134373-160135749	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr3:160127070-160138790	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160131739..160133430-chr3:160134002..160136220,2	MCF-7	breast:

Variant related genes	Relation type
SMC4	TF binding region
ENSG00000113810	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs34182424	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs6768295	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6792810	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7631140	1.00[AFR][1000 genomes]
rs7643188	1.00[AFR][1000 genomes];1.00[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:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160119000-160144600	Weak transcription	Spleen	Spleen
2	chr3:160119000-160145200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:160119400-160137800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr3:160119400-160144400	Weak transcription	Pancreas	Pancrea
5	chr3:160119400-160144600	Weak transcription	Gastric	stomach
6	chr3:160119800-160142000	Weak transcription	Psoas Muscle	Psoas
7	chr3:160119800-160144400	Weak transcription	Esophagus	oesophagus
8	chr3:160119800-160144600	Weak transcription	Lung	lung
9	chr3:160119800-160144600	Weak transcription	Ovary	ovary
10	chr3:160119800-160144600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr3:160119800-160145200	Weak transcription	Brain Hippocampus Middle	brain
12	chr3:160119800-160146600	Weak transcription	HSMMtube	muscle
13	chr3:160119800-160151800	Weak transcription	Brain Substantia Nigra	brain
14	chr3:160120200-160152400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr3:160120200-160164400	Weak transcription	Fetal Brain Male	brain
16	chr3:160121200-160144400	Weak transcription	Colonic Mucosa	Colon
17	chr3:160121200-160157200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr3:160121200-160157400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr3:160121200-160157800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr3:160122000-160139800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr3:160122000-160144800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr3:160122000-160161000	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr3:160122000-160164400	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr3:160122000-160164600	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr3:160122200-160157400	Strong transcription	Fetal Thymus	thymus
26	chr3:160122400-160135000	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr3:160122600-160155000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:160122600-160156600	Strong transcription	K562	blood
29	chr3:160122800-160154200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr3:160123000-160153600	Weak transcription	Brain Anterior Caudate	brain
31	chr3:160123200-160155400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr3:160124000-160159000	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr3:160124200-160152600	Strong transcription	Hela-S3	cervix
34	chr3:160124600-160155000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr3:160125000-160144400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr3:160125200-160159800	Strong transcription	HSMM	muscle
37	chr3:160126800-160137600	Weak transcription	Fetal Heart	heart
38	chr3:160127800-160154000	Strong transcription	HMEC	breast
39	chr3:160127800-160157000	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr3:160128000-160154200	Strong transcription	Dnd41	blood
41	chr3:160128200-160152400	Strong transcription	GM12878-XiMat	blood
42	chr3:160128400-160157200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr3:160128600-160158200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr3:160129000-160141400	Weak transcription	NHLF	lung
45	chr3:160129200-160136400	Strong transcription	NHDF-Ad	bronchial
46	chr3:160129200-160144600	Weak transcription	Brain Cingulate Gyrus	brain
47	chr3:160129400-160149200	Weak transcription	Brain Angular Gyrus	brain
48	chr3:160129600-160151400	Strong transcription	Osteobl	bone
49	chr3:160129600-160156600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:160129600-160157000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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