Variant report

Variant	rs59336221
Chromosome Location	chr1:227834906-227834907
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	chr1:227831322..227834251-chr1:227834809..227836572,2	K562	blood:

Variant related genes	Relation type
ENSG00000181450	Chromatin interaction
ENSG00000265216	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10495277	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10799429	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10799438	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10916172	0.85[ASN][1000 genomes]
rs10916177	0.86[ASN][1000 genomes]
rs1154835	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11805477	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11806830	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11807529	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12120313	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12122398	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12124325	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12126339	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12131517	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12133008	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12135976	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12137033	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12138942	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12141938	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12408514	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1390400	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16848036	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1874371	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1923822	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1951729	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2012386	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2031134	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2093608	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2313245	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2999750	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3010188	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3087908	0.83[EUR][1000 genomes]
rs34901559	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4653851	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4653862	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4653864	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4653865	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55721361	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55841672	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56197655	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56349581	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57346808	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58274339	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60625678	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61322441	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61566561	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6426469	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6667937	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6699448	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs751748	0.83[EUR][1000 genomes]
rs7528010	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9725624	0.86[AMR][1000 genomes];0.96[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs59336221	ZNF678	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227770000-227853800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:227819800-227837600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr1:227820600-227861600	ZNF genes & repeats	Adipose Nuclei	Adipose
4	chr1:227827800-227845400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
5	chr1:227828400-227837400	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
6	chr1:227829400-227859800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:227829600-227837600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
8	chr1:227830800-227845200	ZNF genes & repeats	Dnd41	blood
9	chr1:227831600-227837400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
10	chr1:227831800-227835000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:227831800-227837400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:227831800-227837400	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
13	chr1:227831800-227837600	ZNF genes & repeats	Primary T cells from cord blood	blood
14	chr1:227831800-227839800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
15	chr1:227831800-227840000	ZNF genes & repeats	Primary B cells from cord blood	blood
16	chr1:227831800-227850200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
17	chr1:227831800-227851600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:227831800-227854600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
19	chr1:227831800-227864000	ZNF genes & repeats	Liver	Liver
20	chr1:227832000-227835600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
21	chr1:227832000-227837400	ZNF genes & repeats	Fetal Lung	lung
22	chr1:227832000-227843600	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
23	chr1:227832000-227845200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
24	chr1:227832000-227850200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
25	chr1:227832000-227854400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
26	chr1:227832200-227835800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
27	chr1:227832200-227837400	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
28	chr1:227832200-227850600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:227832400-227835600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:227832400-227837600	ZNF genes & repeats	Brain Hippocampus Middle	brain
31	chr1:227832400-227850400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
32	chr1:227832600-227846400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
33	chr1:227832800-227835200	Weak transcription	HSMM	muscle
34	chr1:227833000-227835000	Weak transcription	Right Ventricle	heart
35	chr1:227833000-227835200	Weak transcription	Rectal Smooth Muscle	rectum
36	chr1:227833000-227835200	Weak transcription	Thymus	Thymus
37	chr1:227833400-227849600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
38	chr1:227833600-227835200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr1:227833600-227835200	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr1:227833600-227837200	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
41	chr1:227833800-227837600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:227833800-227838800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:227834000-227835400	ZNF genes & repeats	Left Ventricle	heart
44	chr1:227834000-227836800	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
45	chr1:227834000-227837000	ZNF genes & repeats	A549	lung
46	chr1:227834000-227837200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:227834000-227837400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr1:227834000-227838000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr1:227834000-227839600	ZNF genes & repeats	Brain Anterior Caudate	brain
50	chr1:227834000-227843800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast

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