Variant report

Variant	rs1045407
Chromosome Location	chr1:227847233-227847234
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:227749302..227751553-chr1:227846304..227849175,2	K562	blood:

Variant related genes	Relation type
ENSG00000181450	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10753436	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753437	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10799422	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10799424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10799428	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10799437	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10799444	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs10916154	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916157	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916160	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916161	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916162	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916163	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916166	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916167	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916189	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916199	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11576992	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11581704	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11590390	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12058246	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12081818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12084072	0.84[EUR][1000 genomes]
rs12092054	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12093031	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12116848	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12119889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12120182	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12123996	0.90[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12129704	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12129894	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12131114	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12132761	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12133625	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12138198	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12138229	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12140813	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12140848	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1390401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1495848	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1845757	0.82[EUR][1000 genomes]
rs1995019	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2172936	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28446171	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2999742	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34421331	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3942992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4379651	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57158394	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61824940	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426470	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6426471	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6426472	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6656661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6659012	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6659349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6669236	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6669277	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6672530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6678802	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6679855	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6689375	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6691443	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6692376	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6694427	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6698409	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74140304	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7418348	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7521812	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7531801	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7538206	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7538893	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7540382	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7540754	0.83[EUR][1000 genomes]
rs7549475	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7551788	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7553531	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs903691	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs951084	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9726691	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1045407	ZNF678	cis	cerebellum	SCAN
rs1045407	TAF5L	cis	parietal	SCAN
rs1045407	JMJD4	cis	multi-tissue	Pritchard

Chromatin state (count:46 , 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	chr1:227831800-227850200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
5	chr1:227831800-227851600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:227831800-227854600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
7	chr1:227831800-227864000	ZNF genes & repeats	Liver	Liver
8	chr1:227832000-227850200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
9	chr1:227832000-227854400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
10	chr1:227832200-227850600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:227832400-227850400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
12	chr1:227833400-227849600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
13	chr1:227835000-227852200	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:227835000-227852600	ZNF genes & repeats	Fetal Brain Female	brain
15	chr1:227835200-227847800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
16	chr1:227836400-227852200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
17	chr1:227838600-227849800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:227838600-227854400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:227838800-227849800	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
20	chr1:227841200-227852000	ZNF genes & repeats	Primary B cells from cord blood	blood
21	chr1:227841200-227852600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
22	chr1:227841200-227852800	ZNF genes & repeats	Brain Anterior Caudate	brain
23	chr1:227841600-227852600	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
24	chr1:227843200-227849400	Weak transcription	Fetal Thymus	thymus
25	chr1:227843200-227851200	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr1:227844200-227847400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:227844400-227847400	ZNF genes & repeats	Brain Hippocampus Middle	brain
28	chr1:227844600-227850800	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr1:227846000-227851600	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
30	chr1:227846200-227847400	ZNF genes & repeats	Ovary	ovary
31	chr1:227846200-227847800	ZNF genes & repeats	Left Ventricle	heart
32	chr1:227846800-227849800	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
33	chr1:227846800-227850400	ZNF genes & repeats	Psoas Muscle	Psoas
34	chr1:227847000-227847400	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
35	chr1:227847000-227847400	ZNF genes & repeats	Pancreas	Pancrea
36	chr1:227847000-227847400	ZNF genes & repeats	Right Atrium	heart
37	chr1:227847000-227847400	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
38	chr1:227847000-227847400	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
39	chr1:227847000-227847600	ZNF genes & repeats	Aorta	Aorta
40	chr1:227847000-227847600	ZNF genes & repeats	HSMMtube	muscle
41	chr1:227847000-227848200	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
42	chr1:227847000-227849600	ZNF genes & repeats	Colon Smooth Muscle	Colon
43	chr1:227847000-227849800	ZNF genes & repeats	A549	lung
44	chr1:227847000-227850200	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
45	chr1:227847000-227850200	ZNF genes & repeats	Dnd41	blood
46	chr1:227847200-227852600	ZNF genes & repeats	Fetal Lung	lung

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