Variant report

Variant	rs61824002
Chromosome Location	chr1:223954904-223954905
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:223950693-223954959	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:223948378..223951598-chr1:223951905..223956257,3	MCF-7	breast:
2	chr1:223946469..223951364-chr1:223952394..223955847,6	K562	blood:
3	chr1:223946962..223949803-chr1:223953280..223955941,2	MCF-7	breast:
4	chr1:223953070..223955896-chr1:224033330..224035597,3	K562	blood:
5	chr1:223952715..223955634-chr1:223956735..223959686,2	MCF-7	breast:

No data

Variant related genes	Relation type
CAPN2	TF binding region
ENSG00000162909	Chromatin interaction
ENSG00000143514	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10799327	0.86[EUR][1000 genomes]
rs10915882	0.86[EUR][1000 genomes]
rs10915892	0.86[EUR][1000 genomes]
rs10915917	0.82[EUR][1000 genomes]
rs1124943	0.89[EUR][1000 genomes]
rs11801971	0.80[EUR][1000 genomes]
rs11806886	0.82[EUR][1000 genomes]
rs12021759	0.83[EUR][1000 genomes]
rs12021785	0.82[EUR][1000 genomes]
rs12024535	0.83[EUR][1000 genomes]
rs12026098	0.83[EUR][1000 genomes]
rs12026835	0.82[EUR][1000 genomes]
rs12027539	0.82[EUR][1000 genomes]
rs12038299	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12040633	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12042503	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12045776	0.86[EUR][1000 genomes]
rs12730520	0.86[EUR][1000 genomes]
rs12731254	0.86[EUR][1000 genomes]
rs17559050	0.86[EUR][1000 genomes]
rs17599	0.96[EUR][1000 genomes]
rs2014441	0.86[EUR][1000 genomes]
rs2126389	0.83[EUR][1000 genomes]
rs34124959	0.83[EUR][1000 genomes]
rs35634773	0.86[EUR][1000 genomes]
rs3856161	0.86[EUR][1000 genomes]
rs4653644	0.82[EUR][1000 genomes]
rs4653645	0.82[EUR][1000 genomes]
rs4653775	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61823593	0.86[EUR][1000 genomes]
rs61823594	0.86[EUR][1000 genomes]
rs61823595	0.86[EUR][1000 genomes]
rs61824006	0.85[EUR][1000 genomes]
rs6658752	0.85[EUR][1000 genomes]
rs6678103	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6688246	0.82[EUR][1000 genomes]
rs6702843	0.83[EUR][1000 genomes]
rs723999	0.83[EUR][1000 genomes]
rs745697	0.86[EUR][1000 genomes]
rs7516059	0.83[EUR][1000 genomes]
rs7519753	0.82[EUR][1000 genomes]
rs7533614	0.86[EUR][1000 genomes]
rs7554109	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv1008800	chr1:223904653-224061032	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223937000-223957200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr1:223937000-223959000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:223937000-223960000	Weak transcription	Thymus	Thymus
4	chr1:223937200-223958400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr1:223937200-223958400	Weak transcription	Fetal Heart	heart
6	chr1:223938600-223956600	Weak transcription	Fetal Kidney	kidney
7	chr1:223939800-223956600	Weak transcription	Fetal Thymus	thymus
8	chr1:223940800-223955000	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr1:223941000-223957600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr1:223941000-223958200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr1:223941000-223959400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr1:223941200-223961600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr1:223942400-223958800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr1:223947000-223957200	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr1:223948000-223957600	Weak transcription	Fetal Brain Male	brain
16	chr1:223948400-223957200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:223949600-223955000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:223949600-223958400	Weak transcription	Small Intestine	intestine
19	chr1:223950000-223957600	Weak transcription	Right Atrium	heart
20	chr1:223950200-223957000	Weak transcription	Psoas Muscle	Psoas
21	chr1:223951400-223957200	Weak transcription	Primary B cells from peripheral blood	blood
22	chr1:223952000-223956800	Weak transcription	Liver	Liver
23	chr1:223952000-223957200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:223952200-223956600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr1:223953200-223956800	Weak transcription	Placenta	Placenta
26	chr1:223953400-223956600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr1:223953600-223956800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:223953600-223956800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr1:223953800-223956600	Weak transcription	Stomach Mucosa	stomach
30	chr1:223953800-223956800	Weak transcription	Aorta	Aorta
31	chr1:223953800-223956800	Weak transcription	Fetal Intestine Large	intestine
32	chr1:223954000-223956600	Weak transcription	Fetal Lung	lung
33	chr1:223954000-223956800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr1:223954000-223957200	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr1:223954200-223956400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr1:223954200-223956600	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr1:223954200-223956600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr1:223954200-223956600	Weak transcription	Brain Anterior Caudate	brain
39	chr1:223954200-223956600	Weak transcription	Colon Smooth Muscle	Colon
40	chr1:223954200-223956600	Weak transcription	Rectal Smooth Muscle	rectum
41	chr1:223954200-223956800	Weak transcription	HUVEC	blood vessel
42	chr1:223954200-223957200	Weak transcription	Brain Angular Gyrus	brain
43	chr1:223954200-223957200	Weak transcription	Brain Germinal Matrix	brain
44	chr1:223954200-223957200	Weak transcription	Brain Hippocampus Middle	brain
45	chr1:223954200-223957400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr1:223954200-223958800	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr1:223954400-223956400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:223954400-223956600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:223954400-223956600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr1:223954400-223956600	Weak transcription	Primary T cells fromperipheralblood	blood

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