Variant report

Variant	rs12656219
Chromosome Location	chr5:179498189-179498190
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:179160317..179162813-chr5:179497518..179499972,2	K562	blood:
2	chr5:154133591..154135701-chr5:179497285..179498805,3	MCF-7	breast:
3	chr5:179233833..179236734-chr5:179497569..179499660,2	MCF-7	breast:
4	chr5:179404319..179405843-chr5:179497809..179500320,2	K562	blood:
5	chr5:179496103..179499035-chr5:179510851..179514542,4	K562	blood:
6	chr5:179467128..179469131-chr5:179495464..179498336,2	MCF-7	breast:
7	chr5:179246093..179248273-chr5:179497691..179500264,2	MCF-7	breast:
8	chr5:179332761..179336643-chr5:179497180..179500753,5	MCF-7	breast:
9	chr5:179285948..179288985-chr5:179497401..179500729,4	K562	blood:
10	chr5:179232651..179234632-chr5:179498072..179500275,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000197226	Chromatin interaction
ENSG00000161013	Chromatin interaction
ENSG00000245317	Chromatin interaction
ENSG00000161011	Chromatin interaction
ENSG00000155506	Chromatin interaction
ENSG00000253480	Chromatin interaction
ENSG00000113269	Chromatin interaction
ENSG00000161021	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10061480	0.87[CHB][hapmap];0.83[ASN][1000 genomes]
rs10068529	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs10068594	0.81[ASN][1000 genomes]
rs10078977	0.81[CHB][hapmap]
rs10903246	0.89[CHD][hapmap]
rs12153541	0.87[CHB][hapmap];0.83[ASN][1000 genomes]
rs12653944	0.86[CHD][hapmap]
rs193718	0.86[CHB][hapmap];0.91[CHD][hapmap];0.87[TSI][hapmap]
rs1961583	0.86[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2009728	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2083968	0.82[AMR][1000 genomes]
rs2120631	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2278661	0.84[CEU][hapmap]
rs2386701	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2386704	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs248316	0.86[CHD][hapmap]
rs27014	0.89[CHD][hapmap]
rs27016	0.88[CHD][hapmap]
rs27017	0.89[ASW][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.80[MEX][hapmap];0.80[MKK][hapmap];0.89[TSI][hapmap]
rs3828698	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4130025	0.87[CHB][hapmap];0.93[CHD][hapmap];0.83[ASN][1000 genomes]
rs4466125	0.83[ASN][1000 genomes]
rs449511	0.89[CHD][hapmap]
rs4700855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4700860	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62405020	0.83[ASN][1000 genomes]
rs62405021	0.83[ASN][1000 genomes]
rs6884290	0.90[ASN][1000 genomes]
rs7728341	0.85[CEU][hapmap];0.80[MEX][hapmap]
rs857181	0.86[CHB][hapmap]
rs9329096	0.83[CHB][hapmap];0.98[CHD][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
2	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
5	nsv830561	chr5:179365637-179537012	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
6	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
7	nsv1024592	chr5:179443133-179510642	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	esv3396669	chr5:179497796-179500194	Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
9	esv3340100	chr5:179497871-179500719	Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12656219	CLTB	cis	parietal	SCAN
rs12656219	MAML1	cis	cerebellum	SCAN
rs12656219	RASGEF1C	cis	parietal	SCAN
rs12656219	RASGEF1C	cis	cerebellum	SCAN
rs12656219	LTC4S	cis	cerebellum	SCAN
rs12656219	BTNL9	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179494800-179498400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr5:179495200-179498400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr5:179495400-179499400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr5:179495600-179499200	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr5:179495800-179499000	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr5:179495800-179499200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr5:179496400-179498400	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr5:179496400-179498400	Bivalent/Poised TSS	GM12878-XiMat	blood
9	chr5:179496600-179498200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr5:179496600-179498200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
11	chr5:179496600-179498400	Flanking Active TSS	K562	blood
12	chr5:179496600-179498400	Flanking Active TSS	NH-A	brain
13	chr5:179496600-179499200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:179496600-179499200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr5:179496600-179499400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr5:179496800-179498200	Flanking Active TSS	Adipose Nuclei	Adipose
17	chr5:179496800-179498200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
18	chr5:179496800-179498400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
19	chr5:179496800-179499200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
20	chr5:179496800-179499400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr5:179496800-179499400	Active TSS	Brain Substantia Nigra	brain
22	chr5:179496800-179499600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr5:179497000-179498200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr5:179497000-179498200	Flanking Active TSS	Osteobl	bone
25	chr5:179497000-179498400	Active TSS	Fetal Brain Male	brain
26	chr5:179497000-179499200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr5:179497000-179499200	Active TSS	Brain Cingulate Gyrus	brain
28	chr5:179497000-179499200	Active TSS	Fetal Muscle Trunk	muscle
29	chr5:179497000-179499400	Active TSS	Cortex derived primary cultured neurospheres	brain
30	chr5:179497000-179499400	Active TSS	Brain Inferior Temporal Lobe	brain
31	chr5:179497200-179498200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr5:179497200-179498200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
33	chr5:179497200-179498200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr5:179497200-179498200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
35	chr5:179497200-179498400	Flanking Active TSS	Primary B cells from peripheral blood	blood
36	chr5:179497200-179499200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr5:179497200-179499200	Active TSS	H9 Cell Line	embryonic stem cell
38	chr5:179497200-179499200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr5:179497200-179499200	Active TSS	Brain Hippocampus Middle	brain
40	chr5:179497200-179499200	Bivalent/Poised TSS	Thymus	Thymus
41	chr5:179497200-179499400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr5:179497200-179499400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr5:179497200-179499400	Active TSS	Fetal Brain Female	brain
44	chr5:179497200-179499400	Active TSS	Left Ventricle	heart
45	chr5:179497200-179499400	Active TSS	Right Ventricle	heart
46	chr5:179497200-179499800	Active TSS	Brain Angular Gyrus	brain
47	chr5:179497200-179499800	Active TSS	Brain Anterior Caudate	brain
48	chr5:179497400-179498200	Active TSS	Colonic Mucosa	Colon
49	chr5:179497400-179498400	Flanking Active TSS	HMEC	breast
50	chr5:179497400-179499200	Active TSS	Primary monocytes fromperipheralblood	blood

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