Variant report

Variant	rs17123307
Chromosome Location	chr1:62737766-62737767
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11803521	0.81[CHB][hapmap];0.82[JPT][hapmap];1.00[ASN][1000 genomes]
rs17123303	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17123306	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17123318	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17123328	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17123329	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3850630	0.86[CHB][hapmap];0.97[ASN][1000 genomes]
rs55812433	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59318560	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59838506	0.97[ASN][1000 genomes]
rs61623093	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1009398	chr1:62656660-62780644	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1013582	chr1:62723703-62910632	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17123307	D4S234E	trans	lymphoblastoid	seeQTL

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62721000-62739400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
2	chr1:62729600-62737800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr1:62732400-62740000	Weak transcription	Liver	Liver
4	chr1:62732400-62748400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:62733000-62741000	Weak transcription	Brain Germinal Matrix	brain
6	chr1:62734200-62750800	Weak transcription	Gastric	stomach
7	chr1:62735800-62740600	Strong transcription	Placenta Amnion	Placenta Amnion
8	chr1:62736200-62739600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:62736400-62738400	Enhancers	Fetal Heart	heart
10	chr1:62736400-62739400	Enhancers	Primary hematopoietic stem cells	blood
11	chr1:62736400-62739400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:62736400-62740400	Enhancers	Fetal Thymus	thymus
13	chr1:62736400-62741000	Strong transcription	HepG2	liver
14	chr1:62736800-62738400	Enhancers	Fetal Muscle Leg	muscle
15	chr1:62736800-62738800	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr1:62736800-62739000	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr1:62736800-62739000	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr1:62736800-62739400	Enhancers	Primary T cells from cord blood	blood
19	chr1:62736800-62739600	Enhancers	Primary T cells fromperipheralblood	blood
20	chr1:62736800-62739600	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr1:62737000-62738000	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr1:62737000-62738000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:62737000-62738400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:62737000-62738400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr1:62737000-62739200	Enhancers	Thymus	Thymus
26	chr1:62737000-62739400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr1:62737000-62740600	Genic enhancers	Fetal Muscle Trunk	muscle
28	chr1:62737200-62737800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:62737200-62738200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr1:62737200-62738400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr1:62737200-62738400	Genic enhancers	Fetal Stomach	stomach
32	chr1:62737200-62738800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr1:62737400-62737800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
34	chr1:62737400-62738000	Enhancers	H9 Cell Line	embryonic stem cell
35	chr1:62737400-62738000	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr1:62737400-62738000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr1:62737400-62738200	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr1:62737400-62738400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr1:62737400-62738400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr1:62737400-62738400	Enhancers	Adipose Nuclei	Adipose
41	chr1:62737400-62738400	Enhancers	Fetal Lung	lung
42	chr1:62737400-62738400	Enhancers	Spleen	Spleen
43	chr1:62737400-62738400	Enhancers	Dnd41	blood
44	chr1:62737400-62738400	Enhancers	GM12878-XiMat	blood
45	chr1:62737400-62739000	Enhancers	Primary B cells from peripheral blood	blood
46	chr1:62737600-62737800	Enhancers	Fetal Intestine Large	intestine
47	chr1:62737600-62737800	Enhancers	Lung	lung
48	chr1:62737600-62737800	Enhancers	Right Atrium	heart
49	chr1:62737600-62738000	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr1:62737600-62738000	Strong transcription	Pancreas	Pancrea

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