Variant report

Variant	rs13150137
Chromosome Location	chr4:57273309-57273310
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:57265970..57269312-chr4:57270989..57273638,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128059	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1042040	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1124570	0.83[ASN][1000 genomes]
rs11538098	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11722404	0.86[ASN][1000 genomes]
rs11728068	0.94[ASN][1000 genomes]
rs11732985	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11734595	0.86[ASN][1000 genomes]
rs11935357	1.00[ASN][1000 genomes]
rs11943048	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13109030	0.91[ASN][1000 genomes]
rs13114481	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13122196	0.80[ASN][1000 genomes]
rs13122422	0.80[ASN][1000 genomes]
rs13122832	0.91[ASN][1000 genomes]
rs13123301	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13123542	0.88[ASN][1000 genomes]
rs13124065	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13129188	0.81[ASN][1000 genomes]
rs13135151	0.80[ASN][1000 genomes]
rs13140746	0.80[ASN][1000 genomes]
rs13146014	0.91[ASN][1000 genomes]
rs13148435	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13148656	0.86[ASN][1000 genomes]
rs13150967	0.91[ASN][1000 genomes]
rs1401911	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17524437	0.82[ASN][1000 genomes]
rs3796544	0.80[ASN][1000 genomes]
rs6554346	0.80[ASN][1000 genomes]
rs6554350	0.80[ASN][1000 genomes]
rs6554353	0.86[ASN][1000 genomes]
rs6554354	0.86[ASN][1000 genomes]
rs6812222	0.80[ASN][1000 genomes]
rs6815480	0.80[ASN][1000 genomes]
rs6818283	0.94[ASN][1000 genomes]
rs6818340	0.94[ASN][1000 genomes]
rs6820922	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6854326	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7654543	1.00[ASN][1000 genomes]
rs7656361	0.80[ASN][1000 genomes]
rs7673373	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7682041	0.83[ASN][1000 genomes]
rs7699157	0.86[ASN][1000 genomes]
rs956275	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13150137	PPAT	Cis_1M	lymphoblastoid	RTeQTL
rs13150137	AASDH	Cis_1M	lymphoblastoid	RTeQTL
rs13150137	AASDH	cis	multi-tissue	Pritchard

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57254200-57273800	Weak transcription	Spleen	Spleen
2	chr4:57254400-57273600	Weak transcription	Pancreas	Pancrea
3	chr4:57254600-57276400	Weak transcription	Psoas Muscle	Psoas
4	chr4:57254600-57280200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr4:57254800-57275200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr4:57254800-57275400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr4:57254800-57276400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr4:57254800-57276400	Weak transcription	Right Ventricle	heart
9	chr4:57254800-57276600	Weak transcription	Left Ventricle	heart
10	chr4:57254800-57287600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr4:57255200-57275600	Weak transcription	NHLF	lung
12	chr4:57255200-57276400	Weak transcription	Colon Smooth Muscle	Colon
13	chr4:57255200-57276600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr4:57255200-57276600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr4:57255200-57276600	Weak transcription	Brain Substantia Nigra	brain
16	chr4:57255400-57276400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr4:57255600-57275600	Weak transcription	Fetal Brain Female	brain
18	chr4:57255800-57276600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr4:57256000-57274200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr4:57256000-57276400	Weak transcription	Brain Hippocampus Middle	brain
21	chr4:57256200-57276600	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr4:57256400-57276600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr4:57257600-57274200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:57258400-57274200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr4:57259000-57274000	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr4:57259400-57275600	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr4:57260200-57274200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr4:57260800-57274200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr4:57262000-57273400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr4:57264000-57274000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr4:57264200-57274000	Strong transcription	GM12878-XiMat	blood
32	chr4:57264200-57290200	Weak transcription	Esophagus	oesophagus
33	chr4:57264400-57276400	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr4:57264800-57301000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr4:57265000-57301000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr4:57265200-57275600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr4:57265400-57273400	Strong transcription	K562	blood
38	chr4:57267200-57275600	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr4:57267400-57274800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr4:57267400-57275400	Weak transcription	NHDF-Ad	bronchial
41	chr4:57267600-57275600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr4:57267600-57275600	Weak transcription	Osteobl	bone
43	chr4:57267600-57276000	Weak transcription	Brain Anterior Caudate	brain
44	chr4:57267600-57276200	Weak transcription	HSMM	muscle
45	chr4:57267600-57276400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr4:57267800-57274200	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr4:57267800-57275000	Weak transcription	Fetal Kidney	kidney
48	chr4:57267800-57277600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr4:57267800-57278400	Weak transcription	Placenta	Placenta
50	chr4:57268000-57275600	Weak transcription	NH-A	brain

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