Variant report

Variant	rs7525020
Chromosome Location	chr1:214636685-214636686
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10494980	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10746445	0.83[CHB][hapmap]
rs10864100	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10864101	0.85[CHB][hapmap];0.82[CHD][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10864102	0.85[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10864103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11120329	0.85[CHB][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11120330	0.85[CHB][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11120331	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11120332	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11120333	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12068677	0.85[CHB][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12096551	0.82[CHB][hapmap]
rs12128034	0.84[CHB][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12739305	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12739336	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12743237	0.85[CHB][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12757384	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12757776	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17023030	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs4145623	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4233301	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4233302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4233303	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4233304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4233305	0.85[CHB][hapmap]
rs4233306	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4253890	0.87[MEX][hapmap]
rs4269744	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[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4284238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4474219	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4480328	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4571940	1.00[CEU][hapmap];0.94[CHD][hapmap];0.80[GIH][hapmap];0.87[JPT][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4655250	0.85[CHB][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4655251	0.85[CHB][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4655252	0.85[CHB][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4655253	0.85[CHB][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4655254	0.85[CHB][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4655255	0.84[CHB][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4655256	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4655258	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4655259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4655347	0.85[CHB][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4655348	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4655349	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4655350	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.84[TSI][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4655351	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4655352	0.85[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4655355	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5020616	0.85[CHB][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5020617	0.85[CHB][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6540830	1.00[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6540835	0.85[CHB][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6540836	0.84[CHB][hapmap]
rs6540838	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6540841	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6661786	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668440	0.85[CHB][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6671350	0.80[CEU][hapmap]
rs6676807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6676956	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6682627	1.00[CEU][hapmap];0.92[MEX][hapmap]
rs6682847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6684018	0.88[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6685434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6689084	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6691633	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7518513	0.83[CHB][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7527320	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7528315	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7531610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7540188	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7540288	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7525020	PTPN14	cis	parietal	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:214613000-214649400	Weak transcription	Lung	lung
2	chr1:214620000-214637400	Weak transcription	Fetal Brain Male	brain
3	chr1:214620800-214636800	Weak transcription	Adipose Nuclei	Adipose
4	chr1:214620800-214637800	Weak transcription	Fetal Muscle Trunk	muscle
5	chr1:214621000-214639800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr1:214625800-214636800	Weak transcription	Esophagus	oesophagus
7	chr1:214625800-214644800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:214627200-214640000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr1:214628400-214636800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr1:214628600-214636800	Weak transcription	Aorta	Aorta
11	chr1:214628600-214636800	Weak transcription	Fetal Muscle Leg	muscle
12	chr1:214628600-214637600	Weak transcription	Ovary	ovary
13	chr1:214628600-214637800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:214628600-214637800	Weak transcription	Placenta	Placenta
15	chr1:214628600-214640600	Weak transcription	Right Atrium	heart
16	chr1:214628800-214636800	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr1:214628800-214639400	Weak transcription	Stomach Mucosa	stomach
18	chr1:214629000-214637800	Weak transcription	Right Ventricle	heart
19	chr1:214629200-214644800	Weak transcription	Psoas Muscle	Psoas
20	chr1:214630400-214637000	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr1:214631800-214637000	Weak transcription	Left Ventricle	heart
22	chr1:214632200-214636800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:214632400-214637000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:214633400-214636800	Strong transcription	HSMM	muscle
25	chr1:214633600-214638000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:214634000-214637000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:214634000-214638600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr1:214634200-214636800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:214634200-214636800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr1:214634200-214637000	Weak transcription	Fetal Intestine Small	intestine
31	chr1:214634200-214638000	Weak transcription	Pancreas	Pancrea
32	chr1:214634200-214640000	Weak transcription	Fetal Kidney	kidney
33	chr1:214634400-214636800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr1:214634400-214636800	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr1:214634400-214637000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr1:214634400-214637800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr1:214634400-214639800	Weak transcription	Fetal Lung	lung
38	chr1:214634400-214639800	Weak transcription	A549	lung
39	chr1:214634400-214640000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr1:214634400-214644400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr1:214634400-214645000	Weak transcription	HUVEC	blood vessel
42	chr1:214634400-214646200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr1:214634600-214637600	Strong transcription	Fetal Stomach	stomach
44	chr1:214634800-214636800	Strong transcription	NH-A	brain
45	chr1:214634800-214637000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr1:214634800-214638200	Strong transcription	Fetal Intestine Large	intestine
47	chr1:214634800-214640000	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr1:214635000-214637800	Weak transcription	Spleen	Spleen
49	chr1:214635000-214638400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:214635000-214638600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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