Variant report

Variant	rs72895894
Chromosome Location	chr3:46916737-46916738
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	chr3:46915275..46917060-chr3:46923765..46925773,2	K562	blood:
2	chr3:46783774..46785518-chr3:46915413..46918248,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PTH1R-1	chr3:46916657-46917160	NONHSAT089463

Variant related genes	Relation type
ENSG00000160801	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12715420	1.00[ASN][1000 genomes]
rs2168442	1.00[ASN][1000 genomes]
rs2233263	1.00[ASN][1000 genomes]
rs35418672	1.00[ASN][1000 genomes]
rs4683305	1.00[ASN][1000 genomes]
rs59227639	1.00[ASN][1000 genomes]
rs7624740	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	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
8	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
9	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
10	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
11	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
12	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
13	nsv876755	chr3:46895109-47061183	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS 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 miRNA target site	25 gene(s)	inside rSNPs	diseases
14	nsv590207	chr3:46903361-46919379	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46906800-46920000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:46909600-46917000	Enhancers	Skeletal Muscle Female	skeletal muscle
3	chr3:46910000-46916800	Weak transcription	Brain Angular Gyrus	brain
4	chr3:46910200-46916800	Weak transcription	Esophagus	oesophagus
5	chr3:46910600-46918400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:46911000-46917200	Enhancers	Right Ventricle	heart
7	chr3:46912200-46921000	Enhancers	Fetal Heart	heart
8	chr3:46912600-46916800	Bivalent Enhancer	Fetal Muscle Leg	muscle
9	chr3:46912600-46917000	Enhancers	Ovary	ovary
10	chr3:46912600-46918600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
11	chr3:46913000-46916800	Enhancers	Lung	lung
12	chr3:46913200-46917400	Bivalent Enhancer	Fetal Stomach	stomach
13	chr3:46913400-46917000	Enhancers	Left Ventricle	heart
14	chr3:46913600-46920200	Weak transcription	Pancreas	Pancrea
15	chr3:46914000-46917600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr3:46914000-46918000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr3:46914200-46917400	Enhancers	Fetal Thymus	thymus
18	chr3:46914200-46918000	Enhancers	Primary hematopoietic stem cells	blood
19	chr3:46914400-46917800	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr3:46914400-46918200	Enhancers	Fetal Kidney	kidney
21	chr3:46914400-46921400	Enhancers	Fetal Intestine Large	intestine
22	chr3:46914600-46919600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:46914800-46917000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:46915400-46917400	Enhancers	Stomach Smooth Muscle	stomach
25	chr3:46915400-46917800	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr3:46915400-46917800	Weak transcription	HSMM	muscle
27	chr3:46915400-46921600	Weak transcription	Brain Hippocampus Middle	brain
28	chr3:46915800-46916800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:46915800-46917000	Weak transcription	Brain Cingulate Gyrus	brain
30	chr3:46915800-46918000	Weak transcription	HSMMtube	muscle
31	chr3:46915800-46923000	Weak transcription	Brain Anterior Caudate	brain
32	chr3:46916000-46921600	Enhancers	Fetal Intestine Small	intestine
33	chr3:46916000-46922400	Weak transcription	Adipose Nuclei	Adipose
34	chr3:46916200-46917000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr3:46916200-46917200	Enhancers	Spleen	Spleen
36	chr3:46916200-46918000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr3:46916200-46918400	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr3:46916400-46916800	Enhancers	Brain Substantia Nigra	brain
39	chr3:46916400-46917800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:46916400-46920200	Weak transcription	Colon Smooth Muscle	Colon
41	chr3:46916600-46916800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
42	chr3:46916600-46916800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr3:46916600-46917000	Flanking Active TSS	Fetal Lung	lung
44	chr3:46916600-46918000	Weak transcription	Placenta	Placenta
45	chr3:46916600-46919200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr3:46916600-46920000	Weak transcription	Right Atrium	heart
47	chr3:46916600-46920200	Weak transcription	Rectal Smooth Muscle	rectum

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