Variant report

Variant	rs60104031
Chromosome Location	chr4:57305939-57305940
allele	C/T
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	POLR2A	chr4:57305896-57306567	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr4:57305901-57306711	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr4:57305833-57306369	HepG2	liver:	n/a	n/a
4	POLR2A	chr4:57305813-57306978	K562	blood:	n/a	n/a
5	POLR2A	chr4:57305769-57306468	SK-N-MC	brain:	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: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10010544	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11133443	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12645138	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1983378	0.82[EUR][1000 genomes]
rs2030366	0.82[EUR][1000 genomes]
rs2271925	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34510373	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3796548	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3822001	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4565139	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56066795	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56356367	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56672277	0.91[ASN][1000 genomes]
rs59997251	0.83[ASN][1000 genomes]
rs67343558	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67721941	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6836118	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6853418	0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs73167398	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7693372	0.81[ASN][1000 genomes]
rs7696808	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs60104031	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	chr4:57303000-57309000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:57303400-57330800	Weak transcription	Spleen	Spleen
3	chr4:57303800-57308400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr4:57303800-57326000	Weak transcription	Gastric	stomach
5	chr4:57303800-57331000	Weak transcription	Stomach Mucosa	stomach
6	chr4:57303800-57332000	Weak transcription	Small Intestine	intestine
7	chr4:57304000-57306800	Enhancers	Liver	Liver
8	chr4:57304000-57312000	Weak transcription	Left Ventricle	heart
9	chr4:57304000-57315800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr4:57304000-57330000	Weak transcription	Pancreas	Pancrea
11	chr4:57304000-57330000	Weak transcription	Right Ventricle	heart
12	chr4:57304000-57331800	Weak transcription	Esophagus	oesophagus
13	chr4:57304200-57306400	Weak transcription	Fetal Muscle Leg	muscle
14	chr4:57304200-57307800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr4:57304200-57307800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr4:57304200-57308000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr4:57304200-57308000	Weak transcription	Placenta	Placenta
18	chr4:57304200-57308200	Weak transcription	Brain Hippocampus Middle	brain
19	chr4:57304200-57314600	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr4:57304200-57314800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr4:57304200-57317400	Weak transcription	Thymus	Thymus
22	chr4:57304200-57318800	Weak transcription	Colon Smooth Muscle	Colon
23	chr4:57304200-57319200	Weak transcription	Stomach Smooth Muscle	stomach
24	chr4:57304200-57331800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr4:57304400-57306000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr4:57304400-57306200	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr4:57304400-57306200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr4:57304400-57306200	Weak transcription	A549	lung
29	chr4:57304400-57306400	Weak transcription	Primary B cells from cord blood	blood
30	chr4:57304400-57306600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr4:57304400-57307000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr4:57304400-57307000	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr4:57304400-57307000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr4:57304400-57307200	Weak transcription	Primary T cells from cord blood	blood
35	chr4:57304400-57307400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr4:57304400-57307600	Weak transcription	Primary hematopoietic stem cells	blood
37	chr4:57304400-57307800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr4:57304400-57307800	Weak transcription	Fetal Brain Male	brain
39	chr4:57304400-57307800	Weak transcription	Fetal Lung	lung
40	chr4:57304400-57307800	Weak transcription	HSMM	muscle
41	chr4:57304400-57307800	Weak transcription	NHDF-Ad	bronchial
42	chr4:57304400-57308000	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr4:57304400-57308000	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr4:57304400-57308000	Weak transcription	Osteobl	bone
45	chr4:57304400-57308200	Weak transcription	Primary B cells from peripheral blood	blood
46	chr4:57304400-57308200	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr4:57304400-57308400	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr4:57304400-57308600	Weak transcription	Brain Anterior Caudate	brain
49	chr4:57304400-57308600	Weak transcription	Fetal Kidney	kidney
50	chr4:57304400-57310400	Weak transcription	NHLF	lung

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