Variant report

Variant	rs17438900
Chromosome Location	chr4:122301622-122301623
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11729700	0.93[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11732033	0.83[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13119176	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13120526	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13120639	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13139657	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13140392	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13146881	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1398908	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs17371707	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap]
rs17371804	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap]
rs17372496	0.82[JPT][hapmap]
rs17437630	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap]
rs17438865	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17439459	1.00[ASN][1000 genomes]
rs1828725	1.00[ASN][1000 genomes]
rs2063682	1.00[ASN][1000 genomes]
rs34480116	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34662155	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34821968	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35097879	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35292409	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35469175	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35623795	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap]
rs35738071	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35870436	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35964783	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6842600	0.93[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs691712	0.85[GIH][hapmap]
rs71602333	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71602335	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7678003	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7688947	0.83[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs964305	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998094	chr4:121504565-122374203	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1009395	chr4:121841442-122557363	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv537235	chr4:121841442-122557363	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv879859	chr4:121892490-122438312	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv817261	chr4:122085173-123020068	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv508308	chr4:122278897-122312719	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17438900	EXOSC9	cis	parietal	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:122300200-122302800	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr4:122300600-122302200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:122300800-122302600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr4:122301000-122302000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
5	chr4:122301000-122302200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr4:122301000-122302200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
7	chr4:122301000-122302400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
8	chr4:122301000-122302400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
9	chr4:122301000-122302400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
10	chr4:122301000-122302600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
11	chr4:122301000-122302600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
12	chr4:122301000-122302600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
13	chr4:122301200-122301800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
14	chr4:122301200-122301800	Enhancers	Pancreas	Pancrea
15	chr4:122301200-122302000	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
16	chr4:122301200-122302000	Bivalent Enhancer	Fetal Heart	heart
17	chr4:122301200-122302400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr4:122301200-122302400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr4:122301200-122302400	Bivalent/Poised TSS	Fetal Lung	lung
20	chr4:122301200-122302400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
21	chr4:122301200-122302400	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
22	chr4:122301400-122301800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr4:122301400-122301800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
24	chr4:122301400-122301800	Enhancers	Aorta	Aorta
25	chr4:122301400-122301800	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
26	chr4:122301400-122301800	Bivalent Enhancer	Placenta	Placenta
27	chr4:122301400-122301800	Flanking Active TSS	Gastric	stomach
28	chr4:122301400-122301800	Flanking Active TSS	Left Ventricle	heart
29	chr4:122301400-122301800	Flanking Active TSS	Right Atrium	heart
30	chr4:122301400-122301800	Flanking Active TSS	Right Ventricle	heart
31	chr4:122301400-122301800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
32	chr4:122301400-122301800	Flanking Bivalent TSS/Enh	NH-A	brain
33	chr4:122301400-122302000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr4:122301400-122302000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
35	chr4:122301400-122302000	Flanking Bivalent TSS/Enh	Brain Angular Gyrus	brain
36	chr4:122301400-122302000	Flanking Bivalent TSS/Enh	NHEK	skin
37	chr4:122301400-122302200	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr4:122301400-122302200	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr4:122301400-122302200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
40	chr4:122301400-122302200	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr4:122301400-122302200	Bivalent/Poised TSS	Brain Substantia Nigra	brain
42	chr4:122301400-122302200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
43	chr4:122301400-122302200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
44	chr4:122301400-122302400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr4:122301400-122302400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr4:122301400-122302400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr4:122301400-122302400	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr4:122301400-122302400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
49	chr4:122301400-122302400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr4:122301400-122302400	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell

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