Variant report

Variant	rs17788590
Chromosome Location	chr1:214598954-214598955
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs12732499	1.00[CHB][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12740482	0.85[AMR][1000 genomes]
rs17022827	1.00[LWK][hapmap];0.89[MKK][hapmap];0.85[YRI][hapmap]
rs17022851	1.00[YRI][hapmap]
rs17022853	1.00[YRI][hapmap]
rs17022856	1.00[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap]
rs17022858	1.00[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap]
rs17022862	0.80[AFR][1000 genomes]
rs17022865	0.80[AFR][1000 genomes]
rs17022866	1.00[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs17022867	0.80[AFR][1000 genomes]
rs17022869	1.00[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs17022870	1.00[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs17022874	0.80[AFR][1000 genomes]
rs17022875	1.00[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs17022877	1.00[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap]
rs17022887	0.80[AFR][1000 genomes]
rs17022892	0.80[AFR][1000 genomes]
rs17732074	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34182952	0.90[ASN][1000 genomes]
rs34415256	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34470079	0.90[ASN][1000 genomes]
rs34607409	0.90[ASN][1000 genomes]
rs35129129	0.95[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs35166549	0.90[ASN][1000 genomes]
rs35226076	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35630729	0.90[ASN][1000 genomes]
rs35646913	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35769201	0.93[ASN][1000 genomes]
rs4604670	1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs61819564	0.90[ASN][1000 genomes]
rs61819565	0.80[AFR][1000 genomes]
rs61819570	0.80[AFR][1000 genomes]
rs61819572	0.96[ASN][1000 genomes]
rs61819573	0.96[ASN][1000 genomes]
rs6540829	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs6700793	1.00[LWK][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs6702991	0.80[AFR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17788590	PTPN14	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:214572600-214612600	Weak transcription	Fetal Intestine Small	intestine
2	chr1:214576800-214612200	Weak transcription	Fetal Intestine Large	intestine
3	chr1:214581400-214601200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:214584200-214603000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr1:214584400-214600000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr1:214591400-214612800	Weak transcription	Pancreas	Pancrea
7	chr1:214591600-214600400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:214591600-214601200	Weak transcription	Gastric	stomach
9	chr1:214591600-214601400	Weak transcription	Lung	lung
10	chr1:214592000-214600200	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr1:214592000-214602200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:214593200-214613000	Weak transcription	Fetal Muscle Leg	muscle
13	chr1:214593400-214602400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:214593400-214612800	Weak transcription	Ovary	ovary
15	chr1:214594000-214618000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr1:214595400-214601200	Weak transcription	Esophagus	oesophagus
17	chr1:214595400-214602400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:214595400-214612800	Weak transcription	Aorta	Aorta
19	chr1:214596000-214614000	Weak transcription	Right Ventricle	heart
20	chr1:214596400-214600200	Weak transcription	Thymus	Thymus
21	chr1:214596400-214601200	Weak transcription	A549	lung
22	chr1:214596600-214599600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr1:214596600-214602400	Enhancers	HMEC	breast
24	chr1:214596600-214603400	Enhancers	NHEK	skin
25	chr1:214596800-214599200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr1:214596800-214599400	Weak transcription	HUVEC	blood vessel
27	chr1:214596800-214601000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr1:214596800-214601200	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr1:214596800-214601200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:214596800-214612800	Weak transcription	Left Ventricle	heart
31	chr1:214597000-214599000	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr1:214597000-214600800	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr1:214597000-214601000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr1:214597000-214601000	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr1:214597000-214601200	Weak transcription	Psoas Muscle	Psoas
36	chr1:214597200-214600800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr1:214597200-214601200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr1:214597200-214604200	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr1:214597600-214601200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr1:214598200-214600400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:214598200-214601000	Enhancers	Muscle Satellite Cultured Cells	--
42	chr1:214598200-214601600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr1:214598200-214601600	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr1:214598200-214603400	Enhancers	HSMM	muscle
45	chr1:214598200-214603400	Enhancers	Osteobl	bone
46	chr1:214598400-214599400	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr1:214598400-214599800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr1:214598400-214599800	Enhancers	Adipose Nuclei	Adipose
49	chr1:214598400-214600200	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr1:214598400-214600400	Enhancers	HSMMtube	muscle

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