Variant report

Variant	rs2363561
Chromosome Location	chr1:215255307-215255308
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF1	chr1:215254974-215255326	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr1:215255216-215255413	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTBP2	chr1:215255151-215256317	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr1:215255248-215255548	H1-hESC	embryonic stem cell:	n/a	n/a
5	TCF12	chr1:215255216-215255450	H1-hESC	embryonic stem cell:	n/a	chr1:215255360-215255370
6	TCF12	chr1:215255214-215255478	H1-hESC	embryonic stem cell:	n/a	chr1:215255360-215255370
7	MAX	chr1:215254986-215255344	H1-hESC	embryonic stem cell:	n/a	chr1:215255128-215255139
8	MAX	chr1:215254963-215255602	H1-hESC	embryonic stem cell:	n/a	chr1:215255128-215255139

Variant related genes	Relation type
KCNK2	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10864151	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[ASN][1000 genomes]
rs11120484	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11120504	0.82[CHB][hapmap]
rs11586565	0.91[ASN][1000 genomes]
rs12041014	0.91[ASN][1000 genomes]
rs2363563	0.82[CHB][hapmap]
rs2885816	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4655271	0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs4655272	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754411	chr1:215235605-215281605	Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2363561	C1orf97	cis	parietal	SCAN
rs2363561	HSPBAP1	trans	parietal	SCAN
rs2363561	SYT14	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:215254800-215255400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr1:215254800-215255400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:215254800-215257400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr1:215254800-215257400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr1:215254800-215259000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:215254800-215260000	Active TSS	Fetal Brain Female	brain
7	chr1:215255000-215255400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:215255000-215255400	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:215255000-215255400	Active TSS	Brain Germinal Matrix	brain
10	chr1:215255000-215255400	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
11	chr1:215255000-215255400	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
12	chr1:215255000-215255400	Bivalent Enhancer	Fetal Muscle Leg	muscle
13	chr1:215255000-215255600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:215255000-215255600	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:215255000-215255600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr1:215255000-215255600	Bivalent Enhancer	Fetal Stomach	stomach
17	chr1:215255000-215255600	Flanking Active TSS	Osteobl	bone
18	chr1:215255000-215255800	Bivalent Enhancer	Primary hematopoietic stem cells	blood
19	chr1:215255000-215256000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:215255000-215256000	Enhancers	Pancreas	Pancrea
21	chr1:215255000-215256200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
22	chr1:215255000-215256800	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
23	chr1:215255000-215257000	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
24	chr1:215255000-215257200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
25	chr1:215255000-215257200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
26	chr1:215255000-215257400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
27	chr1:215255000-215257400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
28	chr1:215255000-215258400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr1:215255200-215255400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr1:215255200-215255400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:215255200-215255400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:215255200-215255400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
33	chr1:215255200-215255400	Active TSS	Brain Angular Gyrus	brain
34	chr1:215255200-215255600	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr1:215255200-215255600	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:215255200-215255600	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:215255200-215255600	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr1:215255200-215255600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
39	chr1:215255200-215255600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
40	chr1:215255200-215255600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr1:215255200-215255800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
42	chr1:215255200-215255800	Bivalent Enhancer	Fetal Lung	lung
43	chr1:215255200-215255800	Flanking Active TSS	NHLF	lung
44	chr1:215255200-215256000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
45	chr1:215255200-215256000	Bivalent Enhancer	Fetal Heart	heart
46	chr1:215255200-215256000	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
47	chr1:215255200-215256000	Flanking Active TSS	NH-A	brain
48	chr1:215255200-215256200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
49	chr1:215255200-215256800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr1:215255200-215256800	Active TSS	Brain Anterior Caudate	brain

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