Variant report

Variant	rs6013844
Chromosome Location	chr20:52565526-52565527
allele	C/T
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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52551745..52571491-chr20:55837843..55848700,39	MCF-7	breast:
2	chr20:52555643..52557522-chr20:52563500..52566122,2	K562	blood:
3	chr17:56707619..56710170-chr20:52565363..52567557,2	MCF-7	breast:
4	chr20:52565008..52572229-chr20:55837900..55845361,9	MCF-7	breast:
5	chr20:52563468..52566159-chr20:52815919..52818201,3	MCF-7	breast:
6	chr17:57919574..57922169-chr20:52565236..52567154,2	MCF-7	breast:
7	chr20:52565056..52568176-chr20:55835450..55837434,3	MCF-7	breast:
8	chr17:59955749..59958529-chr20:52564556..52567164,2	MCF-7	breast:
9	chr20:52563890..52565885-chr20:52722350..52724626,2	MCF-7	breast:
10	chr20:52565026..52565977-chr20:52815663..52816480,2	MCF-7	breast:
11	chr20:52565107..52568649-chr20:52823684..52826196,6	MCF-7	breast:
12	chr17:59938630..59941732-chr20:52564272..52566686,3	MCF-7	breast:
13	chr20:52564545..52567284-chr20:52704374..52707126,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000236352	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000101132	Chromatin interaction
ENSG00000136492	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000101144	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1055249	0.85[ASN][1000 genomes]
rs1055251	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6013845	0.88[ASW][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs6123329	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs719204	0.82[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases
2	nsv834009	chr20:52386050-52590795	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	182 gene(s)	inside rSNPs	diseases
3	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
4	nsv1055549	chr20:52555871-52586281	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6013844	CSTF1	cis	cerebellum	SCAN
rs6013844	FAM65C	cis	parietal	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52552400-52566000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr20:52556600-52566000	Weak transcription	Aorta	Aorta
3	chr20:52557400-52569200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr20:52558000-52565800	Weak transcription	Colonic Mucosa	Colon
5	chr20:52558000-52566000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr20:52558400-52569000	Weak transcription	Fetal Intestine Small	intestine
7	chr20:52560000-52566200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr20:52560800-52565600	Weak transcription	Brain Angular Gyrus	brain
9	chr20:52560800-52565600	Weak transcription	Brain Substantia Nigra	brain
10	chr20:52561000-52565600	Weak transcription	Fetal Heart	heart
11	chr20:52561000-52565600	Weak transcription	Fetal Lung	lung
12	chr20:52561000-52565800	Weak transcription	Brain Anterior Caudate	brain
13	chr20:52561000-52566000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr20:52564000-52567200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr20:52564200-52565600	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr20:52564200-52567400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr20:52564200-52576400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr20:52564400-52565600	Enhancers	GM12878-XiMat	blood
19	chr20:52564600-52565600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr20:52564600-52565600	Strong transcription	Stomach Mucosa	stomach
21	chr20:52564600-52567000	Enhancers	Primary hematopoietic stem cells	blood
22	chr20:52564600-52567400	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr20:52564800-52565600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr20:52564800-52566000	Weak transcription	K562	blood
25	chr20:52564800-52567000	Enhancers	Fetal Thymus	thymus
26	chr20:52565000-52565600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr20:52565000-52565600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr20:52565000-52565600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
29	chr20:52565000-52565800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
30	chr20:52565000-52566000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr20:52565000-52567000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr20:52565000-52567000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr20:52565000-52567000	Enhancers	Primary B cells from peripheral blood	blood
34	chr20:52565000-52567000	Enhancers	Left Ventricle	heart
35	chr20:52565000-52567000	Enhancers	Lung	lung
36	chr20:52565000-52567000	Enhancers	Thymus	Thymus
37	chr20:52565000-52567000	Enhancers	Spleen	Spleen
38	chr20:52565000-52567000	Enhancers	HMEC	breast
39	chr20:52565200-52565600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr20:52565200-52565600	Genic enhancers	HSMMtube	muscle
41	chr20:52565200-52565600	Enhancers	NH-A	brain
42	chr20:52565200-52566000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
43	chr20:52565200-52566000	Enhancers	HSMM	muscle
44	chr20:52565200-52566400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr20:52565200-52566400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
46	chr20:52565200-52566400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
47	chr20:52565200-52566400	Genic enhancers	Rectal Mucosa Donor 29	rectum
48	chr20:52565200-52566400	Enhancers	Small Intestine	intestine
49	chr20:52565200-52566400	Enhancers	Hela-S3	cervix
50	chr20:52565200-52566600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--

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