Variant report

Variant	rs12239497
Chromosome Location	chr1:247011412-247011413
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:247005474..247007845-chr1:247009959..247011844,2	K562	blood:

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs13374054	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1779983	1.00[AMR][1000 genomes]
rs41308156	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59979296	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74152741	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74152745	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74152747	0.97[AFR][1000 genomes];1.00[AMR][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	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv873421	chr1:246818634-247044692	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv2762192	chr1:246823857-247069232	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	nsv1011346	chr1:246868799-247133898	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	esv1810844	chr1:246988018-247054824	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv873424	chr1:246991094-247366380	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 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	chr1:247000200-247020200	Weak transcription	Spleen	Spleen
2	chr1:247001400-247012000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:247001400-247016400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:247001400-247020000	Weak transcription	Brain Substantia Nigra	brain
5	chr1:247002000-247038200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:247002200-247031400	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr1:247002200-247033800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:247002200-247034200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:247002200-247082400	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr1:247002400-247081000	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr1:247002800-247032600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:247002800-247043200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr1:247003000-247015200	Weak transcription	Fetal Heart	heart
14	chr1:247003000-247015200	Weak transcription	NHLF	lung
15	chr1:247003000-247018600	Weak transcription	Fetal Brain Male	brain
16	chr1:247003200-247012000	Weak transcription	Psoas Muscle	Psoas
17	chr1:247003200-247015200	Weak transcription	Esophagus	oesophagus
18	chr1:247003200-247020400	Weak transcription	Gastric	stomach
19	chr1:247003200-247029200	Strong transcription	Fetal Thymus	thymus
20	chr1:247003200-247042200	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr1:247003200-247042800	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr1:247003400-247022600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr1:247003400-247043000	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr1:247003400-247044600	Strong transcription	Dnd41	blood
25	chr1:247004000-247013600	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr1:247004000-247022200	Strong transcription	Fetal Intestine Large	intestine
27	chr1:247004000-247040800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr1:247004000-247041200	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr1:247004000-247042800	Strong transcription	Primary T cells from cord blood	blood
30	chr1:247004000-247053600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:247004200-247011600	Weak transcription	Small Intestine	intestine
32	chr1:247004200-247013000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:247004200-247013000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr1:247004200-247013200	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr1:247004200-247013400	Strong transcription	HSMMtube	muscle
36	chr1:247004200-247018400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr1:247004200-247021200	Strong transcription	A549	lung
38	chr1:247004200-247025200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr1:247004200-247025400	Strong transcription	Fetal Muscle Trunk	muscle
40	chr1:247004200-247042400	Strong transcription	Primary B cells from peripheral blood	blood
41	chr1:247004200-247042800	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr1:247004200-247043000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:247004200-247044400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr1:247004200-247044400	Strong transcription	Liver	Liver
45	chr1:247004200-247083400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:247004400-247012600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
47	chr1:247004400-247013000	Strong transcription	Hela-S3	cervix
48	chr1:247004400-247013200	Strong transcription	HSMM	muscle
49	chr1:247004400-247025200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr1:247004400-247025200	Strong transcription	Rectal Mucosa Donor 29	rectum

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