Variant report

Variant	rs73830478
Chromosome Location	chr3:48733889-48733890
allele	C/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	chr3:48733764-48734149	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr3:48733823-48734313	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr3:48733439-48734449	GM12892	blood:	n/a	n/a
4	POLR2A	chr3:48733879-48734026	HepG2	liver:	n/a	n/a
5	NR3C1	chr3:48733766-48734076	A549	lung:	n/a	chr3:48733840-48733866 chr3:48733840-48733866 chr3:48733840-48733866 chr3:48733840-48733866 chr3:48733846-48733860 chr3:48733845-48733861 chr3:48733840-48733866 chr3:48733844-48733862 chr3:48733845-48733861
6	TCF7L2	chr3:48733687-48733920	MCF-7	breast:	n/a	n/a
7	POLR2A	chr3:48733692-48734338	A549	lung:	n/a	n/a
8	POLR2A	chr3:48733695-48734387	GM12892	blood:	n/a	n/a
9	POLR2A	chr3:48733815-48734419	GM12892	blood:	n/a	n/a
10	POLR2A	chr3:48733620-48734380	HepG2	liver:	n/a	n/a
11	POLR2A	chr3:48733873-48734390	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr3:48733740-48734399	GM12878	blood:	n/a	n/a
13	POLR2A	chr3:48733626-48734321	GM12891	blood:	n/a	n/a
14	POLR2A	chr3:48733696-48734391	GM12891	blood:	n/a	n/a
15	POLR2A	chr3:48733835-48734431	GM12891	blood:	n/a	n/a
16	POLR2A	chr3:48733851-48734227	GM12891	blood:	n/a	n/a
17	POLR2A	chr3:48733494-48734462	GM12878	blood:	n/a	n/a
18	POLR2A	chr3:48733826-48734056	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:48699225..48701604-chr3:48731929..48734312,2	MCF-7	breast:
2	chr3:48732542..48735376-chr3:48750993..48752883,2	K562	blood:
3	chr3:48730035..48731678-chr3:48732538..48734765,2	MCF-7	breast:

Variant related genes	Relation type
IP6K2	TF binding region
ENSG00000228350	Chromatin interaction
ENSG00000068745	Chromatin interaction
ENSG00000008300	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11915428	1.00[EUR][1000 genomes]
rs13318132	1.00[EUR][1000 genomes]
rs14828	1.00[EUR][1000 genomes]
rs28523319	1.00[EUR][1000 genomes]
rs3924179	1.00[EUR][1000 genomes]
rs55782175	1.00[EUR][1000 genomes]
rs58708931	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58835493	1.00[EUR][1000 genomes]
rs58914641	1.00[EUR][1000 genomes]
rs59352296	1.00[EUR][1000 genomes]
rs60338814	1.00[EUR][1000 genomes]
rs60352528	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442122	1.00[EUR][1000 genomes]
rs6791777	1.00[EUR][1000 genomes]
rs72930094	1.00[EUR][1000 genomes]
rs72931155	1.00[EUR][1000 genomes]
rs72931157	1.00[EUR][1000 genomes]
rs72931171	1.00[EUR][1000 genomes]
rs72934791	1.00[EUR][1000 genomes]
rs73830466	1.00[EUR][1000 genomes]
rs73831577	1.00[EUR][1000 genomes]
rs73831579	1.00[EUR][1000 genomes]
rs7633433	1.00[EUR][1000 genomes]
rs898226	1.00[EUR][1000 genomes]
rs9812977	0.83[AFR][1000 genomes]
rs9820609	1.00[EUR][1000 genomes]
rs9860187	1.00[EUR][1000 genomes]
rs9876812	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9882714	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv590247	chr3:48661985-48801929	Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 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	chr3:48724400-48735800	Strong transcription	GM12878-XiMat	blood
2	chr3:48724600-48734000	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr3:48724600-48734000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr3:48724600-48738000	Strong transcription	Thymus	Thymus
5	chr3:48724600-48738400	Strong transcription	Primary hematopoietic stem cells	blood
6	chr3:48724600-48740400	Strong transcription	Primary B cells from cord blood	blood
7	chr3:48724600-48746600	Strong transcription	Fetal Thymus	thymus
8	chr3:48724600-48749000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:48724800-48734000	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr3:48724800-48735800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:48724800-48737600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr3:48724800-48738400	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr3:48725000-48738600	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr3:48725000-48738600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr3:48725000-48740400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr3:48725000-48740800	Strong transcription	Dnd41	blood
17	chr3:48725200-48738600	Strong transcription	Primary B cells from peripheral blood	blood
18	chr3:48725200-48746200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr3:48731000-48734000	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr3:48731200-48735000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr3:48731400-48734400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr3:48732000-48734400	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:48732000-48734400	Genic enhancers	A549	lung
24	chr3:48732200-48734400	Genic enhancers	Fetal Kidney	kidney
25	chr3:48732200-48735200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr3:48732400-48734400	Genic enhancers	Fetal Intestine Large	intestine
27	chr3:48732400-48736400	Genic enhancers	Primary T cells fromperipheralblood	blood
28	chr3:48732600-48734400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr3:48732800-48734200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:48732800-48734200	Genic enhancers	HUVEC	blood vessel
31	chr3:48732800-48734400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr3:48732800-48734400	Enhancers	Pancreas	Pancrea
33	chr3:48732800-48734400	Enhancers	Stomach Mucosa	stomach
34	chr3:48732800-48734400	Genic enhancers	NHEK	skin
35	chr3:48732800-48735400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr3:48732800-48744800	Weak transcription	Small Intestine	intestine
37	chr3:48732800-48745400	Weak transcription	Psoas Muscle	Psoas
38	chr3:48733000-48734000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr3:48733000-48734000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr3:48733000-48734000	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
41	chr3:48733000-48734000	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr3:48733000-48734000	Enhancers	Fetal Brain Male	brain
43	chr3:48733000-48734000	Genic enhancers	HSMM	muscle
44	chr3:48733000-48734000	Enhancers	NHDF-Ad	bronchial
45	chr3:48733000-48734200	Genic enhancers	H1 Cell Line	embryonic stem cell
46	chr3:48733000-48734200	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr3:48733000-48734200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr3:48733000-48734200	Enhancers	Left Ventricle	heart
49	chr3:48733000-48734400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr3:48733000-48734400	Enhancers	Brain Hippocampus Middle	brain

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