Variant report

Variant	rs10175125
Chromosome Location	chr2:55626945-55626946
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10169760	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10185921	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10469925	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10469926	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10469927	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13393046	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13394244	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13397175	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13405484	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13407643	1.00[AMR][1000 genomes]
rs13407739	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13410452	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13414738	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13415672	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs13424427	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9309265	1.00[YRI][hapmap];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	nsv874156	chr2:55474026-55636351	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv874159	chr2:55513738-55636351	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	esv275364	chr2:55621732-55632233	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55542400-55644800	Weak transcription	Primary T cells from cord blood	blood
2	chr2:55555200-55635800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:55579200-55640800	Weak transcription	Fetal Brain Male	brain
4	chr2:55579400-55644400	Weak transcription	Primary B cells from cord blood	blood
5	chr2:55579600-55632200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:55582000-55632400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:55589400-55639400	Weak transcription	Aorta	Aorta
8	chr2:55589600-55628800	Weak transcription	Fetal Thymus	thymus
9	chr2:55589600-55632200	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr2:55591000-55646000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr2:55592000-55635400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr2:55592200-55631800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:55592800-55635600	Weak transcription	HSMMtube	muscle
14	chr2:55593200-55632600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr2:55593800-55631800	Weak transcription	Brain Germinal Matrix	brain
16	chr2:55600600-55631600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:55600800-55629400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr2:55600800-55629400	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr2:55601800-55631000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:55601800-55644600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr2:55602000-55629600	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr2:55602200-55629600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr2:55602400-55629600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:55603600-55629400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr2:55603600-55630200	Weak transcription	NH-A	brain
26	chr2:55606200-55630400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr2:55608600-55630400	Weak transcription	HSMM	muscle
28	chr2:55612600-55629600	Weak transcription	Dnd41	blood
29	chr2:55612600-55630200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr2:55612800-55632000	Weak transcription	Fetal Stomach	stomach
31	chr2:55614200-55632000	Weak transcription	Thymus	Thymus
32	chr2:55616600-55635400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr2:55616600-55635400	Weak transcription	HMEC	breast
34	chr2:55616800-55630200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr2:55616800-55632200	Weak transcription	Hela-S3	cervix
36	chr2:55616800-55642600	Weak transcription	HUVEC	blood vessel
37	chr2:55618200-55635200	Weak transcription	Psoas Muscle	Psoas
38	chr2:55618200-55639400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr2:55618200-55642400	Weak transcription	Fetal Lung	lung
40	chr2:55618400-55627000	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr2:55618600-55636000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr2:55619000-55630200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr2:55619000-55632200	Weak transcription	Fetal Muscle Leg	muscle
44	chr2:55619200-55627200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr2:55619200-55629400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:55619200-55636800	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr2:55619600-55630400	Weak transcription	Primary hematopoietic stem cells	blood
48	chr2:55619600-55632000	Weak transcription	Fetal Muscle Trunk	muscle
49	chr2:55620000-55627400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr2:55622600-55630400	Weak transcription	K562	blood

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