Variant report

Variant	rs7540754
Chromosome Location	chr1:227850588-227850589
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:227849383..227851144-chr1:227857842..227859420,2	K562	blood:
2	chr1:227770918..227773838-chr1:227849267..227851586,2	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1045407	0.83[EUR][1000 genomes]
rs10753437	0.84[EUR][1000 genomes]
rs10799428	0.80[EUR][1000 genomes]
rs10799437	0.83[EUR][1000 genomes]
rs10799444	0.81[EUR][1000 genomes]
rs10916167	0.81[EUR][1000 genomes]
rs10916174	0.96[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916180	0.83[EUR][1000 genomes]
rs10916189	0.83[EUR][1000 genomes]
rs10916199	0.83[EUR][1000 genomes]
rs11576992	0.81[EUR][1000 genomes]
rs11580196	0.87[EUR][1000 genomes]
rs11581704	0.83[EUR][1000 genomes]
rs11588850	0.84[EUR][1000 genomes]
rs12058246	0.81[EUR][1000 genomes]
rs12081818	0.83[EUR][1000 genomes]
rs12119889	0.83[EUR][1000 genomes]
rs12120182	0.85[EUR][1000 genomes]
rs12129704	0.82[EUR][1000 genomes]
rs12129894	0.81[EUR][1000 genomes]
rs12133625	0.83[EUR][1000 genomes]
rs12138198	0.81[EUR][1000 genomes]
rs12138229	0.81[EUR][1000 genomes]
rs12140813	0.81[EUR][1000 genomes]
rs12140848	0.81[EUR][1000 genomes]
rs28446171	0.82[EUR][1000 genomes]
rs34421331	0.82[EUR][1000 genomes]
rs59885016	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61824940	0.82[EUR][1000 genomes]
rs6426470	0.84[EUR][1000 genomes]
rs6426471	0.84[EUR][1000 genomes]
rs6426472	0.81[EUR][1000 genomes]
rs6659012	0.83[EUR][1000 genomes]
rs6659349	0.83[EUR][1000 genomes]
rs6669236	0.83[EUR][1000 genomes]
rs6678802	0.83[EUR][1000 genomes]
rs6679855	0.83[EUR][1000 genomes]
rs6691443	0.84[EUR][1000 genomes]
rs7521812	0.83[EUR][1000 genomes]
rs7538206	0.84[EUR][1000 genomes]
rs7540382	0.84[EUR][1000 genomes]
rs7549475	0.81[EUR][1000 genomes]
rs7553531	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv873246	chr1:227694948-227884465	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	esv3327012	chr1:227741102-227890968	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7540754	ZNF678	Cis_1M	lymphoblastoid	RTeQTL
rs7540754	JMJD4	cis	multi-tissue	Pritchard

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227770000-227853800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:227820600-227861600	ZNF genes & repeats	Adipose Nuclei	Adipose
3	chr1:227829400-227859800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:227831800-227851600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:227831800-227854600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
6	chr1:227831800-227864000	ZNF genes & repeats	Liver	Liver
7	chr1:227832000-227854400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
8	chr1:227832200-227850600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:227835000-227852200	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:227835000-227852600	ZNF genes & repeats	Fetal Brain Female	brain
11	chr1:227836400-227852200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
12	chr1:227838600-227854400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:227841200-227852000	ZNF genes & repeats	Primary B cells from cord blood	blood
14	chr1:227841200-227852600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
15	chr1:227841200-227852800	ZNF genes & repeats	Brain Anterior Caudate	brain
16	chr1:227841600-227852600	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
17	chr1:227843200-227851200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr1:227844600-227850800	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:227846000-227851600	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
20	chr1:227847200-227852600	ZNF genes & repeats	Fetal Lung	lung
21	chr1:227847600-227852000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:227848400-227850600	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
23	chr1:227848400-227850600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:227848400-227851400	ZNF genes & repeats	Stomach Smooth Muscle	stomach
25	chr1:227848400-227852000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
26	chr1:227848600-227851400	ZNF genes & repeats	Left Ventricle	heart
27	chr1:227848600-227851400	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
28	chr1:227848600-227852400	ZNF genes & repeats	Brain Cingulate Gyrus	brain
29	chr1:227848600-227852400	ZNF genes & repeats	Fetal Muscle Trunk	muscle
30	chr1:227848600-227853200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
31	chr1:227848800-227851000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:227848800-227852600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
33	chr1:227848800-227853400	ZNF genes & repeats	Brain Hippocampus Middle	brain
34	chr1:227849000-227850600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:227849000-227850800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
36	chr1:227849000-227851000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
37	chr1:227849000-227852400	ZNF genes & repeats	Fetal Muscle Leg	muscle
38	chr1:227849000-227853000	ZNF genes & repeats	Brain Substantia Nigra	brain
39	chr1:227849200-227850800	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
40	chr1:227849200-227851600	ZNF genes & repeats	Rectal Smooth Muscle	rectum
41	chr1:227849400-227852600	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
42	chr1:227849800-227851000	Weak transcription	Pancreas	Pancrea
43	chr1:227849800-227851400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr1:227850000-227850600	Weak transcription	Fetal Heart	heart
45	chr1:227850400-227851800	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood

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