Variant report

Variant	rs6580653
Chromosome Location	chr12:48553709-48553710
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48495831..48503326-chr12:48548997..48555180,8	K562	blood:

Variant related genes	Relation type
ENSG00000152556	Chromatin interaction
ENSG00000079387	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10492080	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10783230	0.87[ASN][1000 genomes]
rs10783231	0.91[ASN][1000 genomes]
rs10783232	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10783233	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10875751	0.84[ASN][1000 genomes]
rs11168449	0.88[ASN][1000 genomes]
rs11168451	0.88[ASN][1000 genomes]
rs11168455	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11609399	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11613781	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs12822085	0.88[ASN][1000 genomes]
rs2409001	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4075913	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4141065	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4760620	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4760683	0.82[ASN][1000 genomes]
rs4760685	0.87[ASN][1000 genomes]
rs4760692	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4760698	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs57655233	0.91[ASN][1000 genomes]
rs58331734	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6580656	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6580657	0.87[ASN][1000 genomes]
rs6580660	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs726354	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs72644845	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs72644846	0.89[ASN][1000 genomes]
rs7305418	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7313023	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7315258	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7485057	0.91[ASN][1000 genomes]
rs7485824	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs757556	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7969749	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs879242	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer 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	57 gene(s)	inside rSNPs	diseases
3	nsv508673	chr12:48489786-48567138	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS 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	39 gene(s)	inside rSNPs	diseases
5	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6580653	ZNF641	cis	Whole Blood	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48551800-48554000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr12:48551800-48554400	Weak transcription	Brain Germinal Matrix	brain
3	chr12:48552000-48553800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr12:48552000-48554000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr12:48552000-48554000	Weak transcription	Brain Hippocampus Middle	brain
6	chr12:48552000-48554400	Weak transcription	Brain Anterior Caudate	brain
7	chr12:48552000-48554600	Weak transcription	Fetal Lung	lung
8	chr12:48552000-48554600	Weak transcription	Fetal Muscle Trunk	muscle
9	chr12:48552000-48555800	Enhancers	Primary hematopoietic stem cells	blood
10	chr12:48552000-48556600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr12:48552000-48557800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr12:48552200-48553800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr12:48552200-48553800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr12:48552200-48554000	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr12:48552200-48554000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr12:48552200-48554000	Weak transcription	Fetal Heart	heart
17	chr12:48552200-48554200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr12:48552200-48554600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr12:48552200-48554600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr12:48552200-48554600	Weak transcription	Esophagus	oesophagus
21	chr12:48552200-48554600	Weak transcription	Fetal Thymus	thymus
22	chr12:48552200-48554600	Weak transcription	Psoas Muscle	Psoas
23	chr12:48552200-48554600	Weak transcription	K562	blood
24	chr12:48552200-48554800	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr12:48552200-48554800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr12:48552200-48556600	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr12:48552800-48554600	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr12:48552800-48556000	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr12:48553200-48554600	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr12:48553200-48554600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr12:48553400-48553800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr12:48553400-48553800	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr12:48553400-48553800	Weak transcription	GM12878-XiMat	blood

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