Variant report

Variant	rs4560336
Chromosome Location	chr3:46451358-46451359
allele	G/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	chr3:46450527-46452937	K562	blood:	n/a	n/a
2	SPI1	chr3:46451302-46451535	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:46447015..46450131-chr3:46450692..46453311,4	K562	blood:

Variant related genes	Relation type
ENSG00000223552	TF binding region
ENSG00000121797	Chromatin interaction
ENSG00000223552	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11266744	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11574433	0.96[AFR][1000 genomes]
rs11575815	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11575816	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1800023	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1800874	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2187674	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2213290	0.82[AFR][1000 genomes]
rs2254089	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2734225	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2734648	0.82[EUR][1000 genomes]
rs2856757	0.82[AFR][1000 genomes]
rs2856764	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2856765	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3087252	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3181039	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3204849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34682274	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4683220	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4683222	0.85[ASN][1000 genomes]
rs4683223	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66484806	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs916091	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][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	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv3323840	chr3:46352348-46497196	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv3389382	chr3:46352798-46496696	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46438800-46459800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:46448200-46452000	Enhancers	Dnd41	blood
3	chr3:46448600-46460000	Weak transcription	Gastric	stomach
4	chr3:46449200-46451400	Weak transcription	Brain Hippocampus Middle	brain
5	chr3:46449200-46451800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr3:46449400-46453000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:46449600-46452000	Enhancers	K562	blood
8	chr3:46449600-46453800	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr3:46449600-46454000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:46449600-46457600	Weak transcription	Primary B cells from cord blood	blood
11	chr3:46449800-46451400	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr3:46449800-46451800	Enhancers	Primary hematopoietic stem cells	blood
13	chr3:46449800-46452000	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr3:46449800-46453800	Weak transcription	Small Intestine	intestine
15	chr3:46450000-46451600	Weak transcription	Brain Anterior Caudate	brain
16	chr3:46450000-46451600	Weak transcription	Spleen	Spleen
17	chr3:46450000-46457600	Weak transcription	Stomach Mucosa	stomach
18	chr3:46450000-46457800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr3:46450200-46451400	Weak transcription	Right Ventricle	heart
20	chr3:46450200-46451800	Weak transcription	Right Atrium	heart
21	chr3:46450200-46451800	Weak transcription	HSMMtube	muscle
22	chr3:46450200-46452200	Weak transcription	Placenta	Placenta
23	chr3:46450200-46452400	Weak transcription	NHLF	lung
24	chr3:46450200-46452800	Weak transcription	Colonic Mucosa	Colon
25	chr3:46450200-46454200	Weak transcription	Fetal Lung	lung
26	chr3:46450200-46456800	Weak transcription	Fetal Intestine Large	intestine
27	chr3:46450200-46457400	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr3:46450200-46457600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr3:46450400-46451600	Weak transcription	Fetal Heart	heart
30	chr3:46450400-46452200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:46450400-46452600	Enhancers	Thymus	Thymus
32	chr3:46450400-46454200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr3:46450600-46451400	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr3:46450600-46451600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr3:46450600-46451600	Weak transcription	Left Ventricle	heart
36	chr3:46450600-46451600	Weak transcription	HSMM	muscle
37	chr3:46450600-46451800	Weak transcription	Osteobl	bone
38	chr3:46450600-46454000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:46450600-46454000	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr3:46450600-46457000	Weak transcription	Duodenum Mucosa	Duodenum
41	chr3:46450800-46451800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr3:46450800-46452200	Enhancers	Primary T cells from cord blood	blood
43	chr3:46450800-46453600	Weak transcription	HUVEC	blood vessel
44	chr3:46450800-46454000	Weak transcription	Psoas Muscle	Psoas
45	chr3:46451000-46451800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr3:46451000-46451800	Strong transcription	Fetal Intestine Small	intestine
47	chr3:46451000-46452000	Genic enhancers	Lung	lung
48	chr3:46451000-46452400	Enhancers	Fetal Thymus	thymus
49	chr3:46451000-46457600	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr3:46451200-46451400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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