Variant report

Variant	rs12239040
Chromosome Location	chr1:224320226-224320227
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:224319528..224321607-chr1:224321881..224324191,2	K562	blood:
2	chr1:224313532..224316324-chr1:224319519..224321918,2	K562	blood:
3	chr1:224316899..224321028-chr1:224322259..224326330,4	K562	blood:
4	chr1:224318706..224320701-chr1:224370372..224372701,2	K562	blood:

Variant related genes	Relation type
ENSG00000143753	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10916423	1.00[ASN][1000 genomes]
rs57105953	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57441274	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59738860	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60172546	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60877434	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60998173	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs61022093	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6681511	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73122502	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73124408	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73124414	0.93[AFR][1000 genomes]
rs73124430	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73124458	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73124460	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73124474	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73124499	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73126403	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73126432	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7546034	0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv427941	chr1:224085052-224363163	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv832692	chr1:224206536-224407717	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv873222	chr1:224292898-224335422	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224302800-224327200	Weak transcription	Aorta	Aorta
2	chr1:224303000-224329000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:224303000-224363400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:224314400-224333800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:224314400-224343400	Weak transcription	Psoas Muscle	Psoas
6	chr1:224315800-224331200	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr1:224316400-224331200	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr1:224316600-224352200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr1:224317200-224329800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr1:224317600-224320800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:224317600-224321000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr1:224317600-224328400	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr1:224317600-224333400	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr1:224317800-224320800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
15	chr1:224317800-224320800	Strong transcription	K562	blood
16	chr1:224317800-224321000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:224317800-224321000	Strong transcription	Ovary	ovary
18	chr1:224317800-224321000	Strong transcription	Thymus	Thymus
19	chr1:224317800-224321400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:224317800-224322600	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr1:224317800-224323000	Strong transcription	Dnd41	blood
22	chr1:224317800-224325000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr1:224317800-224328200	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr1:224317800-224328400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr1:224317800-224334000	Strong transcription	Fetal Intestine Large	intestine
26	chr1:224318000-224320400	Strong transcription	Fetal Muscle Leg	muscle
27	chr1:224318000-224320400	Strong transcription	Hela-S3	cervix
28	chr1:224318000-224320600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:224318000-224320800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:224318000-224320800	Strong transcription	HSMMtube	muscle
31	chr1:224318000-224321000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:224318000-224321000	Strong transcription	Brain Angular Gyrus	brain
33	chr1:224318000-224321000	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr1:224318000-224321000	Strong transcription	Fetal Brain Male	brain
35	chr1:224318000-224321200	Strong transcription	Primary T cells from cord blood	blood
36	chr1:224318000-224323000	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr1:224318000-224323400	Strong transcription	Liver	Liver
38	chr1:224318000-224324200	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr1:224318000-224324200	Strong transcription	HepG2	liver
40	chr1:224318000-224324400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr1:224318000-224328400	Strong transcription	Primary B cells from peripheral blood	blood
42	chr1:224318000-224328400	Strong transcription	Fetal Thymus	thymus
43	chr1:224318000-224328600	Strong transcription	Duodenum Mucosa	Duodenum
44	chr1:224318000-224329600	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr1:224318000-224330600	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr1:224318000-224331200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr1:224318000-224332000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr1:224318200-224320400	Strong transcription	Placenta	Placenta
49	chr1:224318200-224320400	Strong transcription	Right Ventricle	heart
50	chr1:224318200-224320800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood

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