Variant report

Variant	rs7974817
Chromosome Location	chr12:21587483-21587484
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:21587445-21587495	GM12878	blood:	n/a
2	chr12:21587445-21587495	NH-A	brain:	n/a
3	chr12:21587445-21587495	PFSK-1	brain:	n/a
4	chr12:21587445-21587495	BE2_C	brain:	n/a
5	chr12:21587445-21587495	IMR90	lung:	fetal
6	chr12:21587445-21587495	BJ	skin:	n/a
7	chr12:21587445-21587495	LNCaP	prostate:	n/a
8	chr12:21587445-21587495	CMK	blood:	n/a
9	chr12:21587445-21587495	HRE	kidney:	n/a
10	chr12:21587445-21587495	HL-60	blood:	n/a
11	chr12:21587445-21587495	GM12891	blood:	n/a
12	chr12:21587445-21587495	Jurkat	blood:	n/a
13	chr12:21587445-21587495	NHDF-neo	bronchial:	n/a
14	chr12:21587445-21587495	HEEpiC	esophagus:	n/a
15	chr12:21587445-21587495	HNPCEpiC	eye:	n/a
16	chr12:21587445-21587495	HAEpiC	amniotic membrane:	n/a
17	chr12:21587445-21587495	ovcar-3	ovarian:	n/a
18	chr12:21587445-21587495	H1-hESC	embryonic stem cell:	embryo
19	chr12:21587445-21587495	AoSMC	blood vessel:	n/a
20	chr12:21587445-21587495	SK-N-MC	brain:	n/a
21	chr12:21587445-21587495	SK-N-SH_RA	brain:	n/a
22	chr12:21587445-21587495	GM06990	blood:	n/a
23	chr12:21587445-21587495	GM19239	blood:	n/a
24	chr12:21587445-21587495	ECC-1	luminal epithelium:	n/a
25	chr12:21587445-21587495	MCF10A-Er-Src	breast:	n/a
26	chr12:21587445-21587495	U87	brain:	n/a
27	chr12:21587445-21587495	T-47D	breast:	n/a
28	chr12:21587445-21587495	Hela-S3	cervix:	n/a
29	chr12:21587445-21587495	HEK293	kidney:	embryo
30	chr12:21587445-21587495	MCF-7	breast:	n/a
31	chr12:21587445-21587495	ProgFib	skin:	n/a
32	chr12:21587445-21587495	NB4	blood:	n/a
33	chr12:21587445-21587495	GM12892	blood:	n/a
34	chr12:21587445-21587495	HCT-116	colon:	n/a
35	chr12:21587445-21587495	PrEC	prostate:	n/a
36	chr12:21587445-21587495	SKMC	muscle:	n/a
37	chr12:21587445-21587495	HPAEpiC	pulmonary alveolar:	n/a
38	chr12:21587445-21587495	NHBE	bronchial:	n/a
39	chr12:21587445-21587495	AG10803	skin:	n/a
40	chr12:21587445-21587495	SK-N-SH	brain:	n/a
41	chr12:21587445-21587495	K562	blood:	n/a
42	chr12:21587445-21587495	SAEC	small airway:	n/a
43	chr12:21587445-21587495	HRCEpiC	kidney:	n/a
44	chr12:21587445-21587495	AG09309	skin:	n/a
45	chr12:21587445-21587495	AG04449	skin:	fetal
46	chr12:21587445-21587495	PANC-1	pancreas:	n/a
47	chr12:21587445-21587495	A549	lung:	n/a
48	chr12:21587445-21587495	HMEC	breast:	n/a
49	chr12:21587445-21587495	HUVEC	blood vessel:	n/a
50	chr12:21587445-21587495	Caco-2	colon:	n/a

No data

Variant related genes	Relation type
PYROXD1	CpG island

Extended variants
information (count: 42 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1024734	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11046040	0.85[ASN][1000 genomes]
rs11046044	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11611002	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap]
rs11835956	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12422251	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12423173	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12423381	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12423536	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12424852	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12426100	0.87[CHB][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12426103	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12817513	0.87[CHB][hapmap];0.84[ASN][1000 genomes]
rs12818516	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12826040	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1860948	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2110164	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2417987	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4539382	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4762826	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6487224	0.91[CEU][hapmap];0.93[YRI][hapmap]
rs7131809	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7133131	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7133853	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7138089	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7298136	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7310391	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7314131	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs738027	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7957415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7959893	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7971245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973116	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7974260	0.86[CEU][hapmap]
rs9668302	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526789	chr12:21555691-21590788	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
2	nsv898895	chr12:21561645-21621891	Weak transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
3	nsv898896	chr12:21561645-21695584	Strong transcription Bivalent Enhancer Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1043936	chr12:21562673-21979030	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv557741	chr12:21578559-22169854	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv469163	chr12:21579080-21592357	Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
7	nsv557742	chr12:21579080-21592357	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7974817	PYROXD1	Cis_1M	lymphoblastoid	RTeQTL
rs7974817	FLJ22028	cis	normal skin	skin_eQTL
rs7974817	LOC642732	Cis_1M	lymphoblastoid	RTeQTL
rs7974817	IAPP	cis	uninvolved skin	skin_eQTL
rs7974817	PYROXD1	cis	Esophagus Muscularis	GTEx
rs7974817	LOC642732///PYROXD1	Cis_1M	lymphoblastoid	RTeQTL
rs7974817	RECQL	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21581800-21590000	Weak transcription	HUVEC	blood vessel
2	chr12:21587200-21590200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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