Variant report

Variant	rs1356787
Chromosome Location	chr4:57305202-57305203
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr4:57305033-57305233	MCF10A-Er-Src	breast:	n/a	chr4:57305160-57305171 chr4:57305135-57305144
2	FOS	chr4:57305032-57305223	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr4:57305013-57305284	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr4:57305139-57305211	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:57268050..57270580-chr4:57305183..57307241,2	K562	blood:
2	chr4:57298117..57310780-chr4:57324651..57337770,39	MCF-7	breast:

Variant related genes	Relation type
PPAT	TF binding region
ENSG00000174780	Chromatin interaction
ENSG00000270109	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10009543	0.87[EUR][1000 genomes]
rs10015221	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs1060472	0.88[MEX][hapmap]
rs10866433	0.90[YRI][hapmap];0.83[AFR][1000 genomes]
rs11133439	0.91[JPT][hapmap]
rs11133442	0.88[MEX][hapmap]
rs11610	0.87[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.88[MEX][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11724302	0.95[JPT][hapmap]
rs12498340	0.80[MEX][hapmap]
rs12504291	0.80[CEU][hapmap];0.80[JPT][hapmap]
rs12646703	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12648503	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs13141793	0.91[JPT][hapmap]
rs17051687	1.00[CEU][hapmap];0.92[TSI][hapmap]
rs17086696	0.80[MEX][hapmap]
rs17086793	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs17086803	0.90[YRI][hapmap];0.83[AFR][1000 genomes]
rs17086883	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17086887	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1967559	0.84[MEX][hapmap]
rs2049087	0.89[TSI][hapmap]
rs2292985	0.95[JPT][hapmap]
rs4383672	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4524447	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4615235	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4616819	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4865090	0.95[JPT][hapmap]
rs4865102	0.87[EUR][1000 genomes]
rs4865104	0.81[AFR][1000 genomes]
rs4865105	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4865110	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs57523479	0.89[ASN][1000 genomes]
rs58975286	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6554348	0.95[JPT][hapmap]
rs6554349	0.95[JPT][hapmap]
rs6584	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];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66599079	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs68101565	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6811482	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6816268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6818715	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6819534	1.00[CEU][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs6820417	0.86[ASN][1000 genomes]
rs6830518	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6832168	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6842307	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6848187	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.88[MEX][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7664841	0.80[MEX][hapmap]
rs7670198	0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7689163	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7692073	0.87[EUR][1000 genomes]
rs7692385	0.95[JPT][hapmap]
rs7693137	0.95[JPT][hapmap]
rs7694047	0.90[EUR][1000 genomes]
rs8340	0.80[MEX][hapmap]
rs9996593	0.89[TSI][hapmap]

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	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1356787	AASDH	cis	parietal	SCAN
rs1356787	AASDH	cis	cerebellum	SCAN
rs1356787	SRP72	cis	cerebellum	SCAN
rs1356787	PAICS	cis	cerebellum	SCAN
rs1356787	SRP72	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57298400-57305600	Active TSS	Hela-S3	cervix
2	chr4:57299200-57305800	Active TSS	H1 Cell Line	embryonic stem cell
3	chr4:57299200-57305800	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr4:57299200-57305800	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr4:57299800-57305600	Active TSS	HepG2	liver
6	chr4:57303000-57309000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr4:57303400-57330800	Weak transcription	Spleen	Spleen
8	chr4:57303800-57308400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr4:57303800-57326000	Weak transcription	Gastric	stomach
10	chr4:57303800-57331000	Weak transcription	Stomach Mucosa	stomach
11	chr4:57303800-57332000	Weak transcription	Small Intestine	intestine
12	chr4:57304000-57305800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr4:57304000-57306800	Enhancers	Liver	Liver
14	chr4:57304000-57312000	Weak transcription	Left Ventricle	heart
15	chr4:57304000-57315800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr4:57304000-57330000	Weak transcription	Pancreas	Pancrea
17	chr4:57304000-57330000	Weak transcription	Right Ventricle	heart
18	chr4:57304000-57331800	Weak transcription	Esophagus	oesophagus
19	chr4:57304200-57305600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:57304200-57305800	Weak transcription	Brain Angular Gyrus	brain
21	chr4:57304200-57305800	Weak transcription	Fetal Thymus	thymus
22	chr4:57304200-57306400	Weak transcription	Fetal Muscle Leg	muscle
23	chr4:57304200-57307800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr4:57304200-57307800	Weak transcription	Fetal Muscle Trunk	muscle
25	chr4:57304200-57308000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr4:57304200-57308000	Weak transcription	Placenta	Placenta
27	chr4:57304200-57308200	Weak transcription	Brain Hippocampus Middle	brain
28	chr4:57304200-57314600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr4:57304200-57314800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr4:57304200-57317400	Weak transcription	Thymus	Thymus
31	chr4:57304200-57318800	Weak transcription	Colon Smooth Muscle	Colon
32	chr4:57304200-57319200	Weak transcription	Stomach Smooth Muscle	stomach
33	chr4:57304200-57331800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr4:57304400-57305400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr4:57304400-57305400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr4:57304400-57305400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr4:57304400-57305400	Weak transcription	Brain Germinal Matrix	brain
38	chr4:57304400-57305600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr4:57304400-57305600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr4:57304400-57305600	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr4:57304400-57305600	Weak transcription	Fetal Intestine Small	intestine
42	chr4:57304400-57305800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr4:57304400-57305800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr4:57304400-57305800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr4:57304400-57305800	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr4:57304400-57305800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr4:57304400-57305800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr4:57304400-57305800	Weak transcription	Duodenum Mucosa	Duodenum
49	chr4:57304400-57305800	Weak transcription	Fetal Intestine Large	intestine
50	chr4:57304400-57305800	Weak transcription	HMEC	breast

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