Variant report

Variant	rs56387622
Chromosome Location	chr3:46888198-46888199
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:46882754..46884665-chr3:46886091..46888357,2	K562	blood:
2	chr3:46732249..46733917-chr3:46887547..46889689,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1077216	0.96[ASN][1000 genomes]
rs2242118	0.84[ASN][1000 genomes]
rs3729704	0.85[ASN][1000 genomes]
rs3792557	0.85[ASN][1000 genomes]
rs61351097	0.99[ASN][1000 genomes]
rs66668401	0.95[ASN][1000 genomes]
rs67529903	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6768627	0.95[ASN][1000 genomes]
rs6768845	0.95[ASN][1000 genomes]
rs6778660	0.95[ASN][1000 genomes]
rs6781266	0.95[ASN][1000 genomes]
rs6786689	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6787229	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72895203	0.95[ASN][1000 genomes]
rs73065118	0.81[ASN][1000 genomes]
rs73065135	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73065147	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007449	chr3:46652343-46986578	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv536554	chr3:46652343-46986578	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	esv2757869	chr3:46680452-46972489	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	esv2759147	chr3:46680452-46972489	Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv536558	chr3:46706571-47024756	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv915922	chr3:46768104-47009805	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv590204	chr3:46852679-46901654	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv590205	chr3:46852679-46929546	Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv1003979	chr3:46853374-46943854	Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv590206	chr3:46873957-46935527	Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv876752	chr3:46879831-46967040	Bivalent/Poised TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv876753	chr3:46884552-46957298	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	nsv876754	chr3:46884552-46967040	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs56387622	PRSS45	cis	Thyroid	GTEx
rs56387622	PRSS46	cis	Thyroid	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46886400-46888200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr3:46886600-46888200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr3:46886600-46888200	Flanking Active TSS	Adipose Nuclei	Adipose
4	chr3:46886600-46888200	Enhancers	Fetal Heart	heart
5	chr3:46886600-46888200	Active TSS	Fetal Kidney	kidney
6	chr3:46886600-46888400	Enhancers	Fetal Brain Male	brain
7	chr3:46886800-46888200	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr3:46886800-46888200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
9	chr3:46886800-46888200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
10	chr3:46886800-46888200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr3:46886800-46888200	Flanking Active TSS	HUVEC	blood vessel
12	chr3:46886800-46888400	Flanking Active TSS	Right Ventricle	heart
13	chr3:46887000-46888200	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:46887000-46888200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
15	chr3:46887000-46888200	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr3:46887200-46888200	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:46887200-46888200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:46887200-46889200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:46887200-46890800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr3:46887400-46888200	Enhancers	HSMMtube	muscle
21	chr3:46887400-46888400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:46887400-46888600	Enhancers	Lung	lung
23	chr3:46887400-46890200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:46887600-46888200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr3:46887600-46888200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
26	chr3:46887600-46888200	Flanking Active TSS	Colonic Mucosa	Colon
27	chr3:46887600-46888400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr3:46887600-46888600	Enhancers	Placenta Amnion	Placenta Amnion
29	chr3:46887800-46888200	Flanking Active TSS	Primary T cells from cord blood	blood
30	chr3:46887800-46888200	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
31	chr3:46887800-46888200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr3:46887800-46888200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
33	chr3:46887800-46888200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr3:46887800-46888200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
35	chr3:46887800-46888200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr3:46887800-46888200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
37	chr3:46887800-46888200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr3:46887800-46888200	Flanking Active TSS	Brain Hippocampus Middle	brain
39	chr3:46887800-46888200	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
40	chr3:46887800-46888200	Flanking Active TSS	Pancreas	Pancrea
41	chr3:46887800-46888200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
42	chr3:46887800-46888200	Flanking Active TSS	Rectal Smooth Muscle	rectum
43	chr3:46887800-46888200	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr3:46887800-46888200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
45	chr3:46887800-46888200	Flanking Active TSS	GM12878-XiMat	blood
46	chr3:46887800-46888200	Flanking Active TSS	K562	blood
47	chr3:46887800-46888200	Flanking Active TSS	NH-A	brain
48	chr3:46887800-46888200	Flanking Active TSS	NHLF	lung
49	chr3:46887800-46888200	Flanking Active TSS	Osteobl	bone
50	chr3:46887800-46888400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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