Variant report

Variant	rs12715420
Chromosome Location	chr3:46952777-46952778
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:46751310..46753575-chr3:46950623..46952874,2	K562	blood:
2	chr3:46942624..46944169-chr3:46950936..46952777,2	MCF-7	breast:
3	chr3:46951194..46952854-chr3:46962905..46965136,2	MCF-7	breast:
4	chr3:46950867..46953146-chr3:46955719..46957284,2	K562	blood:

Variant related genes	Relation type
ENSG00000160801	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs13060505	1.00[CEU][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs2168442	1.00[ASN][1000 genomes]
rs2233263	1.00[ASN][1000 genomes]
rs33983156	1.00[EUR][1000 genomes]
rs34207078	1.00[EUR][1000 genomes]
rs35194354	0.89[EUR][1000 genomes]
rs35418672	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35512962	1.00[EUR][1000 genomes]
rs4683305	1.00[ASN][1000 genomes]
rs59227639	1.00[ASN][1000 genomes]
rs71327102	0.83[EUR][1000 genomes]
rs71328903	0.83[EUR][1000 genomes]
rs72895894	1.00[ASN][1000 genomes]
rs7624740	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7651753	1.00[CEU][hapmap]
rs9841902	1.00[CEU][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
8	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
9	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
10	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
11	nsv460526	chr3:46935527-47001350	Genic enhancers Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46950400-46954600	Weak transcription	Fetal Heart	heart
2	chr3:46950400-46958800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:46950600-46961800	Weak transcription	Aorta	Aorta
4	chr3:46951000-46957400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:46951000-46959000	Weak transcription	Fetal Brain Female	brain
6	chr3:46951200-46955000	Weak transcription	Right Atrium	heart
7	chr3:46951200-46955000	Weak transcription	HUVEC	blood vessel
8	chr3:46951200-46955200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr3:46951200-46955200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr3:46951200-46955400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:46951200-46956600	Weak transcription	Thymus	Thymus
12	chr3:46951200-46957800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:46951200-46958200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:46951200-46958400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:46951200-46958600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:46951200-46958600	Weak transcription	Brain Germinal Matrix	brain
17	chr3:46951200-46958600	Weak transcription	Fetal Brain Male	brain
18	chr3:46951200-46960400	Weak transcription	Colonic Mucosa	Colon
19	chr3:46951400-46955000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr3:46951400-46955000	Weak transcription	Stomach Smooth Muscle	stomach
21	chr3:46951400-46955000	Weak transcription	Hela-S3	cervix
22	chr3:46951400-46955200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:46951400-46955200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr3:46951400-46955200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr3:46951400-46955200	Weak transcription	Liver	Liver
26	chr3:46951400-46955200	Weak transcription	Brain Anterior Caudate	brain
27	chr3:46951400-46955200	Weak transcription	Duodenum Mucosa	Duodenum
28	chr3:46951400-46955200	Weak transcription	Fetal Lung	lung
29	chr3:46951400-46955200	Weak transcription	Pancreas	Pancrea
30	chr3:46951400-46955200	Weak transcription	Right Ventricle	heart
31	chr3:46951400-46956600	Weak transcription	Primary hematopoietic stem cells	blood
32	chr3:46951400-46956800	Weak transcription	Primary T cells from cord blood	blood
33	chr3:46951400-46957800	Weak transcription	Primary B cells from cord blood	blood
34	chr3:46951400-46958200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr3:46951400-46958400	Weak transcription	Fetal Kidney	kidney
36	chr3:46951400-46961600	Weak transcription	Stomach Mucosa	stomach
37	chr3:46951600-46953000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:46951600-46954400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr3:46951600-46954600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr3:46951600-46954800	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr3:46951600-46955000	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr3:46951600-46955000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr3:46951600-46955000	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr3:46951600-46955000	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr3:46951600-46955000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr3:46951600-46955000	Weak transcription	Adipose Nuclei	Adipose
47	chr3:46951600-46955000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr3:46951600-46955000	Weak transcription	Gastric	stomach
49	chr3:46951600-46955000	Weak transcription	Left Ventricle	heart
50	chr3:46951600-46955000	Weak transcription	Rectal Mucosa Donor 31	rectum

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