Variant report

Variant	rs6554356
Chromosome Location	chr4:57274679-57274680
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10015221	0.90[JPT][hapmap]
rs10015634	0.89[JPT][hapmap]
rs10031012	0.82[EUR][1000 genomes]
rs10031550	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10034154	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10518	0.89[JPT][hapmap]
rs10866433	0.90[JPT][hapmap]
rs11133438	0.80[EUR][1000 genomes]
rs11133439	0.87[CEU][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs11724302	0.88[CEU][hapmap];0.92[YRI][hapmap];0.80[EUR][1000 genomes]
rs11733474	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12331363	0.80[EUR][1000 genomes]
rs12331412	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13114104	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13133016	0.89[EUR][1000 genomes]
rs13141793	0.95[CEU][hapmap];0.87[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13147824	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1356788	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1401907	0.80[CEU][hapmap]
rs1401912	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1464286	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1474178	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17051687	0.89[JPT][hapmap]
rs17086803	0.90[JPT][hapmap]
rs1976815	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1996650	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2030365	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2049087	0.94[JPT][hapmap]
rs2139512	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2292985	0.87[CEU][hapmap]
rs28559894	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2899063	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3796542	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3796547	0.87[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3822003	0.87[CEU][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes]
rs4073691	0.94[JPT][hapmap]
rs4167	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4305581	0.94[JPT][hapmap]
rs4865087	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4865090	0.86[CEU][hapmap];0.87[YRI][hapmap]
rs4865100	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4865101	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57503982	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59615456	0.81[EUR][1000 genomes]
rs62310633	0.83[EUR][1000 genomes]
rs6554348	0.87[CEU][hapmap];0.86[YRI][hapmap]
rs6554349	1.00[CEU][hapmap];0.88[YRI][hapmap];0.89[EUR][1000 genomes]
rs6554352	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6554355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6811821	0.89[JPT][hapmap]
rs6812041	0.92[CHB][hapmap];0.86[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6819534	0.94[JPT][hapmap]
rs6826795	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6841016	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6841053	0.80[ASN][1000 genomes]
rs6856845	0.81[EUR][1000 genomes]
rs7657711	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7661712	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7683781	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7692385	1.00[CEU][hapmap];0.88[YRI][hapmap];0.88[EUR][1000 genomes]
rs7693137	0.87[CEU][hapmap];0.87[YRI][hapmap]
rs7693683	0.92[EUR][1000 genomes]
rs7700034	0.84[JPT][hapmap]
rs9312674	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9683679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9684298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9993277	0.83[CEU][hapmap]
rs9996593	0.89[JPT][hapmap]
rs9997639	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[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	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv4347	chr4:57261404-57280595	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv1801975	chr4:57267406-57297335	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6554356	PPAT	cis	uninvolved skin	skin_eQTL
rs6554356	PPAT	cis	lesional skin	skin_eQTL
rs6554356	PPAT	Cis_1M	lymphoblastoid	RTeQTL
rs6554356	PPAT	cis	normal skin	skin_eQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57254600-57276400	Weak transcription	Psoas Muscle	Psoas
2	chr4:57254600-57280200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr4:57254800-57275200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr4:57254800-57275400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr4:57254800-57276400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr4:57254800-57276400	Weak transcription	Right Ventricle	heart
7	chr4:57254800-57276600	Weak transcription	Left Ventricle	heart
8	chr4:57254800-57287600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr4:57255200-57275600	Weak transcription	NHLF	lung
10	chr4:57255200-57276400	Weak transcription	Colon Smooth Muscle	Colon
11	chr4:57255200-57276600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr4:57255200-57276600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr4:57255200-57276600	Weak transcription	Brain Substantia Nigra	brain
14	chr4:57255400-57276400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr4:57255600-57275600	Weak transcription	Fetal Brain Female	brain
16	chr4:57255800-57276600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr4:57256000-57276400	Weak transcription	Brain Hippocampus Middle	brain
18	chr4:57256200-57276600	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr4:57256400-57276600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr4:57259400-57275600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr4:57264200-57290200	Weak transcription	Esophagus	oesophagus
22	chr4:57264400-57276400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr4:57264800-57301000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr4:57265000-57301000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr4:57265200-57275600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr4:57267200-57275600	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr4:57267400-57274800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr4:57267400-57275400	Weak transcription	NHDF-Ad	bronchial
29	chr4:57267600-57275600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr4:57267600-57275600	Weak transcription	Osteobl	bone
31	chr4:57267600-57276000	Weak transcription	Brain Anterior Caudate	brain
32	chr4:57267600-57276200	Weak transcription	HSMM	muscle
33	chr4:57267600-57276400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr4:57267800-57275000	Weak transcription	Fetal Kidney	kidney
35	chr4:57267800-57277600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr4:57267800-57278400	Weak transcription	Placenta	Placenta
37	chr4:57268000-57275600	Weak transcription	NH-A	brain
38	chr4:57269600-57275400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr4:57270200-57276800	Weak transcription	Colonic Mucosa	Colon
40	chr4:57272000-57275600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr4:57272000-57276200	Weak transcription	Fetal Intestine Large	intestine
42	chr4:57272000-57276400	Weak transcription	HSMMtube	muscle
43	chr4:57272200-57275000	Weak transcription	Fetal Stomach	stomach
44	chr4:57272200-57275200	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr4:57272200-57275400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr4:57272200-57275600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr4:57272200-57276400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr4:57272200-57276400	Weak transcription	Aorta	Aorta
49	chr4:57272200-57276400	Weak transcription	Ovary	ovary
50	chr4:57272200-57276600	Weak transcription	Fetal Intestine Small	intestine

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