Variant report

Variant	rs12644152
Chromosome Location	chr4:88313179-88313180
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA2	chr4:88311780-88313183	SH-SY5Y	brain:	n/a	chr4:88312660-88312676
2	CEBPB	chr4:88313006-88313704	K562	blood:	n/a	n/a
3	NR2F2	chr4:88311975-88313236	K562	blood:	n/a	n/a
4	MXI1	chr4:88310607-88313452	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr4:88312089-88313200	K562	blood:	n/a	n/a
6	IRF1	chr4:88311875-88313220	K562	blood:	n/a	chr4:88311981-88311995
7	RCOR1	chr4:88312008-88313183	K562	blood:	n/a	n/a
8	GATA3	chr4:88312731-88313179	SH-SY5Y	brain:	n/a	n/a
9	POLR2A	chr4:88311940-88313216	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:88293477..88300868-chr4:88308814..88313684,7	K562	blood:
2	chr4:88311663..88314102-chr4:88359641..88363442,4	K562	blood:
3	chr4:88139395..88142439-chr4:88311139..88313328,4	K562	blood:
4	chr4:88309813..88313902-chr4:88342245..88346379,5	K562	blood:
5	chr4:88310329..88313185-chr4:88330457..88332566,2	K562	blood:
6	chr4:88310667..88314164-chr4:88342247..88345345,4	K562	blood:

No data

Variant related genes	Relation type
HSD17B11	TF binding region
RN7SL681P	TF binding region
ENSG00000170502	Chromatin interaction
ENSG00000249262	Chromatin interaction
ENSG00000145332	Chromatin interaction
ENSG00000198189	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11097154	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11097155	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11934698	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13134730	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13134914	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13143137	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13143153	1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34208894	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34239468	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35856555	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6531990	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6837468	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6842852	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6844669	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71607425	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71607431	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs71607432	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71607434	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71607435	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7689678	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004518	chr4:88218473-88354403	Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv1002789	chr4:88239340-88606485	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12644152	NUDT9	cis	lymphoblastoid	seeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88309000-88313200	Active TSS	Rectal Smooth Muscle	rectum
2	chr4:88309600-88313200	Active TSS	Psoas Muscle	Psoas
3	chr4:88309600-88313200	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr4:88309600-88313400	Active TSS	Stomach Smooth Muscle	stomach
5	chr4:88309800-88313200	Active TSS	Right Atrium	heart
6	chr4:88310000-88313200	Active TSS	Brain Anterior Caudate	brain
7	chr4:88310000-88313400	Active TSS	K562	blood
8	chr4:88310400-88313200	Active TSS	Left Ventricle	heart
9	chr4:88310600-88313200	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr4:88310600-88313200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:88310600-88313200	Active TSS	A549	lung
12	chr4:88310600-88313400	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr4:88310800-88313200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr4:88310800-88313200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr4:88310800-88313200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr4:88310800-88313200	Active TSS	Brain Angular Gyrus	brain
17	chr4:88310800-88313200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr4:88310800-88313200	Active TSS	Brain Substantia Nigra	brain
19	chr4:88310800-88313200	Active TSS	Ovary	ovary
20	chr4:88310800-88313200	Active TSS	Right Ventricle	heart
21	chr4:88311000-88313200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr4:88311000-88313200	Active TSS	Duodenum Mucosa	Duodenum
23	chr4:88311000-88313200	Active TSS	Skeletal Muscle Male	skeletal muscle
24	chr4:88311000-88313200	Active TSS	HSMM	muscle
25	chr4:88311000-88313400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr4:88311200-88313200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr4:88311200-88313200	Active TSS	Primary T helper naive cells from peripheral blood	blood
28	chr4:88311200-88313200	Active TSS	Placenta	Placenta
29	chr4:88311200-88313200	Active TSS	HSMMtube	muscle
30	chr4:88311400-88313200	Active TSS	H9 Cell Line	embryonic stem cell
31	chr4:88311400-88313200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr4:88311400-88313200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr4:88311400-88313200	Active TSS	Aorta	Aorta
34	chr4:88311400-88313400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr4:88311600-88313200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
36	chr4:88311600-88313200	Active TSS	Fetal Muscle Trunk	muscle
37	chr4:88311600-88313200	Active TSS	Thymus	Thymus
38	chr4:88311600-88313200	Active TSS	NH-A	brain
39	chr4:88311600-88313400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr4:88311800-88313200	Active TSS	H1 Cell Line	embryonic stem cell
41	chr4:88311800-88313200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr4:88311800-88313200	Active TSS	Fetal Brain Male	brain
43	chr4:88312600-88313200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
44	chr4:88312600-88313200	Flanking Active TSS	Primary hematopoietic stem cells	blood
45	chr4:88312600-88313200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
46	chr4:88312600-88313200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr4:88312600-88313200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr4:88312600-88313200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
49	chr4:88312600-88313600	Flanking Active TSS	Primary B cells from cord blood	blood
50	chr4:88312800-88313200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell

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