Variant report

Variant	rs17362128
Chromosome Location	chr1:179114803-179114804
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1004959	0.81[ASN][1000 genomes]
rs10157885	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10158768	0.88[ASN][1000 genomes]
rs10913687	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs11808217	1.00[JPT][hapmap]
rs12066589	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12071751	1.00[JPT][hapmap]
rs12076957	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12080991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12083856	1.00[JPT][hapmap]
rs12143004	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17277358	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17361990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2017688	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2274228	0.85[ASN][1000 genomes]
rs2274230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28459842	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28914474	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28914485	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3753532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766631	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs3766633	1.00[JPT][hapmap]
rs3766634	1.00[JPT][hapmap]
rs45499094	0.85[ASN][1000 genomes]
rs55642919	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55825882	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55827544	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55920203	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55955319	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56382583	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60741626	0.86[ASN][1000 genomes]
rs60826716	0.86[ASN][1000 genomes]
rs6668200	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs6669988	0.86[ASN][1000 genomes]
rs7516491	1.00[JPT][hapmap]
rs9650997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9650998	0.96[EUR][1000 genomes]
rs9724754	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9725888	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs9726948	1.00[JPT][hapmap]
rs9730271	0.88[ASN][1000 genomes]
rs9803885	0.87[EUR][1000 genomes];0.86[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	nsv1012667	chr1:179094571-179120280	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1002253	chr1:179094571-179120938	Strong transcription Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1001191	chr1:179097246-179120938	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv1009493	chr1:179110523-179121079	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179093400-179117200	Weak transcription	Fetal Stomach	stomach
2	chr1:179099600-179116800	Weak transcription	Thymus	Thymus
3	chr1:179099600-179119400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:179099600-179122600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr1:179100000-179121000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr1:179100600-179117200	Weak transcription	Fetal Intestine Small	intestine
7	chr1:179107600-179119800	Weak transcription	Liver	Liver
8	chr1:179110000-179118400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:179110200-179116000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:179110200-179121400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr1:179111000-179118200	Weak transcription	Primary B cells from cord blood	blood
12	chr1:179111400-179116400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr1:179111400-179117400	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr1:179111400-179118400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:179111400-179121400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr1:179111400-179121400	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr1:179112200-179118800	Weak transcription	Fetal Intestine Large	intestine
18	chr1:179112200-179121800	Weak transcription	Adipose Nuclei	Adipose
19	chr1:179112200-179121800	Weak transcription	Colon Smooth Muscle	Colon
20	chr1:179112200-179124600	Weak transcription	Left Ventricle	heart
21	chr1:179112400-179115800	Weak transcription	NHLF	lung
22	chr1:179112400-179116200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr1:179112400-179117200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:179112400-179117400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:179112400-179117400	Weak transcription	Primary hematopoietic stem cells	blood
26	chr1:179112400-179117600	Weak transcription	Right Ventricle	heart
27	chr1:179112400-179118400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr1:179112400-179119600	Weak transcription	HepG2	liver
29	chr1:179112400-179121000	Weak transcription	Primary B cells from peripheral blood	blood
30	chr1:179112400-179121200	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr1:179112400-179121400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr1:179112400-179121400	Weak transcription	Small Intestine	intestine
33	chr1:179112400-179121600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr1:179112400-179133000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr1:179112400-179139000	Weak transcription	K562	blood
36	chr1:179112600-179116400	Enhancers	Muscle Satellite Cultured Cells	--
37	chr1:179112800-179115000	Enhancers	NH-A	brain
38	chr1:179112800-179115200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr1:179112800-179116200	Enhancers	NHDF-Ad	bronchial
40	chr1:179112800-179116200	Enhancers	NHEK	skin
41	chr1:179112800-179116800	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr1:179112800-179117200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr1:179112800-179119000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr1:179113000-179115000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr1:179113200-179116200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr1:179113200-179116800	Enhancers	HUVEC	blood vessel
47	chr1:179113200-179133000	Weak transcription	Hela-S3	cervix
48	chr1:179113600-179115600	Weak transcription	HMEC	breast
49	chr1:179113600-179117400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr1:179113600-179121600	Weak transcription	Ovary	ovary

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