Variant report

Variant	rs498041
Chromosome Location	chr2:169730643-169730644
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	chr2:169728195..169733629-chr2:169741403..169748359,8	K562	blood:

Variant related genes	Relation type
ENSG00000152253	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10084216	0.86[AFR][1000 genomes]
rs2685800	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2685801	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs475467	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs477309	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs479661	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs494859	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs499160	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs504393	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs509988	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs511778	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs525428	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs533492	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs534771	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs539400	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs560494	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs576338	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs577192	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs580507	0.96[EUR][1000 genomes]
rs581363	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv583599	chr2:169664227-169903096	Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats 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	12 gene(s)	inside rSNPs	diseases
2	nsv875381	chr2:169686559-169749841	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:169698600-169744600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:169702200-169733000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr2:169709800-169733400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr2:169713400-169731200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:169714000-169732800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr2:169715400-169731600	Weak transcription	Small Intestine	intestine
7	chr2:169715400-169746200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr2:169716000-169745800	Weak transcription	HSMM	muscle
9	chr2:169717000-169746400	Weak transcription	Primary B cells from cord blood	blood
10	chr2:169719800-169733600	Weak transcription	NHDF-Ad	bronchial
11	chr2:169722000-169730800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr2:169722000-169730800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr2:169722000-169732800	Weak transcription	Fetal Heart	heart
14	chr2:169722000-169736200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr2:169722000-169741200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr2:169722000-169741400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr2:169722000-169741400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr2:169722000-169741400	Weak transcription	NHEK	skin
19	chr2:169722000-169741800	Weak transcription	Fetal Lung	lung
20	chr2:169722000-169742800	Weak transcription	Fetal Muscle Trunk	muscle
21	chr2:169722000-169744000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:169722000-169745800	Weak transcription	Fetal Stomach	stomach
23	chr2:169722000-169745800	Weak transcription	GM12878-XiMat	blood
24	chr2:169722000-169746000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr2:169722000-169746000	Weak transcription	Fetal Intestine Large	intestine
26	chr2:169722000-169746000	Weak transcription	Fetal Intestine Small	intestine
27	chr2:169722000-169746000	Weak transcription	Fetal Muscle Leg	muscle
28	chr2:169722200-169730800	Weak transcription	Duodenum Mucosa	Duodenum
29	chr2:169722200-169741400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr2:169724000-169733200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr2:169727600-169733800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr2:169727800-169731000	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr2:169727800-169731200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr2:169727800-169731800	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr2:169727800-169732200	Strong transcription	Fetal Thymus	thymus
36	chr2:169728000-169731400	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr2:169728000-169731600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr2:169728000-169731800	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr2:169728000-169733800	Strong transcription	K562	blood
40	chr2:169728000-169734000	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr2:169728200-169734000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:169728600-169733200	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr2:169728600-169741400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr2:169729000-169736400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr2:169729200-169731000	Weak transcription	Primary hematopoietic stem cells	blood
46	chr2:169729200-169732200	Strong transcription	Dnd41	blood
47	chr2:169729200-169733200	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr2:169729600-169741600	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr2:169729600-169745800	Weak transcription	Thymus	Thymus
50	chr2:169730000-169736400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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