Variant report

Variant	rs7680878
Chromosome Location	chr4:88344651-88344652
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:88310667..88314164-chr4:88342247..88345345,4	K562	blood:
2	chr4:88344098..88346850-chr4:88347399..88349099,3	MCF-7	breast:
3	chr4:88340563..88342774-chr4:88344260..88346848,4	MCF-7	breast:
4	chr4:88309813..88313902-chr4:88342245..88346379,5	K562	blood:

Variant related genes	Relation type
ENSG00000198189	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10000196	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10009948	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10023606	0.91[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10024781	0.95[ASN][1000 genomes]
rs10030035	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10032122	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10084883	0.98[ASN][1000 genomes]
rs12640451	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12640894	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12648665	0.82[AMR][1000 genomes]
rs12650763	0.98[ASN][1000 genomes]
rs12651034	0.98[ASN][1000 genomes]
rs28366407	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs28415220	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28437709	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28493315	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28493566	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28529046	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs28535549	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28696943	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28712618	0.98[ASN][1000 genomes]
rs28718986	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28762371	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28805573	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs34027531	0.87[ASN][1000 genomes]
rs4411944	0.87[ASN][1000 genomes]
rs55824708	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56153912	1.00[ASN][1000 genomes]
rs58192677	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67121411	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs68045074	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72652067	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7665115	0.98[ASN][1000 genomes]
rs7673763	1.00[CEU][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7677249	0.98[ASN][1000 genomes]
rs7690728	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9995987	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9998212	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7680878	NUDT9	cis	brain	BrainEAC
rs7680878	HSD17B11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88342400-88344800	Active TSS	Brain Anterior Caudate	brain
2	chr4:88342400-88345400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:88342400-88345400	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr4:88342600-88345000	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr4:88342600-88345400	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr4:88342600-88345400	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr4:88342600-88346000	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr4:88342800-88344800	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr4:88342800-88344800	Active TSS	Brain Hippocampus Middle	brain
10	chr4:88342800-88345000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr4:88342800-88345000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr4:88342800-88345000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr4:88342800-88345000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr4:88343000-88344800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr4:88343000-88344800	Active TSS	Brain Inferior Temporal Lobe	brain
16	chr4:88343000-88344800	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr4:88343000-88344800	Active TSS	Rectal Smooth Muscle	rectum
18	chr4:88343000-88344800	Active TSS	A549	lung
19	chr4:88343000-88344800	Active TSS	HMEC	breast
20	chr4:88343000-88344800	Active TSS	NHEK	skin
21	chr4:88343000-88345000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr4:88343000-88345000	Active TSS	Colonic Mucosa	Colon
23	chr4:88343000-88345000	Active TSS	HSMMtube	muscle
24	chr4:88343000-88345000	Active TSS	NHDF-Ad	bronchial
25	chr4:88343000-88345200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr4:88343000-88345200	Active TSS	NHLF	lung
27	chr4:88343000-88345400	Active TSS	H9 Cell Line	embryonic stem cell
28	chr4:88343000-88345400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr4:88343000-88345400	Active TSS	Ovary	ovary
30	chr4:88343000-88345800	Active TSS	HSMM	muscle
31	chr4:88343200-88344800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr4:88343200-88344800	Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr4:88343200-88344800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr4:88343200-88344800	Active TSS	Brain Angular Gyrus	brain
35	chr4:88343200-88344800	Active TSS	Fetal Heart	heart
36	chr4:88343200-88344800	Active TSS	Skeletal Muscle Male	skeletal muscle
37	chr4:88343200-88345000	Active TSS	Left Ventricle	heart
38	chr4:88343200-88345000	Active TSS	Psoas Muscle	Psoas
39	chr4:88343200-88345000	Active TSS	Right Atrium	heart
40	chr4:88343200-88345000	Active TSS	Right Ventricle	heart
41	chr4:88343200-88345200	Active TSS	Aorta	Aorta
42	chr4:88343200-88345200	Active TSS	GM12878-XiMat	blood
43	chr4:88343200-88345400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr4:88343200-88345400	Active TSS	HUES48 Cell Line	embryonic stem cell
45	chr4:88343200-88345800	Active TSS	Fetal Kidney	kidney
46	chr4:88343200-88345800	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr4:88343400-88344800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr4:88343400-88344800	Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr4:88343400-88344800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr4:88343400-88344800	Active TSS	Primary T cells fromperipheralblood	blood

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