Variant report

Variant	rs6426468
Chromosome Location	chr1:227834400-227834401
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1056699	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1060295	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10799430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10799439	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10916171	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10916188	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10916191	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10916203	0.89[CEU][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1111046	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs1155807	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12025942	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12033000	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12033610	0.86[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1810680	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1923823	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2104245	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2132368	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2172937	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2236360	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2236361	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4500311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4653856	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6426473	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6660432	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6693054	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6703846	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs730684	0.86[ASW][hapmap];0.89[CEU][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7522634	0.81[EUR][1000 genomes]
rs7526184	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7533588	0.92[CEU][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7534403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7536765	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7539282	0.96[CEU][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9786978	0.86[ASW][hapmap];0.89[CEU][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap]

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
rs6426468	ZNF678	cis	cerebellum	SCAN
rs6426468	ZNF678	cis	normal skin	skin_eQTL

Chromatin state (count:73 , 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	chr1:227790400-227834800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:227819800-227837600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr1:227820600-227861600	ZNF genes & repeats	Adipose Nuclei	Adipose
5	chr1:227827800-227845400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
6	chr1:227828400-227837400	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
7	chr1:227829400-227859800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:227829600-227837600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
9	chr1:227830800-227845200	ZNF genes & repeats	Dnd41	blood
10	chr1:227831600-227837400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
11	chr1:227831800-227834400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
12	chr1:227831800-227835000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:227831800-227837400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:227831800-227837400	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
15	chr1:227831800-227837600	ZNF genes & repeats	Primary T cells from cord blood	blood
16	chr1:227831800-227839800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
17	chr1:227831800-227840000	ZNF genes & repeats	Primary B cells from cord blood	blood
18	chr1:227831800-227850200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
19	chr1:227831800-227851600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:227831800-227854600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
21	chr1:227831800-227864000	ZNF genes & repeats	Liver	Liver
22	chr1:227832000-227834800	ZNF genes & repeats	Fetal Muscle Trunk	muscle
23	chr1:227832000-227835600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
24	chr1:227832000-227837400	ZNF genes & repeats	Fetal Lung	lung
25	chr1:227832000-227843600	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
26	chr1:227832000-227845200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
27	chr1:227832000-227850200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
28	chr1:227832000-227854400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
29	chr1:227832200-227835800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
30	chr1:227832200-227837400	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
31	chr1:227832200-227850600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr1:227832400-227835600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:227832400-227837600	ZNF genes & repeats	Brain Hippocampus Middle	brain
34	chr1:227832400-227850400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
35	chr1:227832600-227846400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
36	chr1:227832800-227835200	Weak transcription	HSMM	muscle
37	chr1:227833000-227834600	Weak transcription	Ovary	ovary
38	chr1:227833000-227835000	Weak transcription	Right Ventricle	heart
39	chr1:227833000-227835200	Weak transcription	Rectal Smooth Muscle	rectum
40	chr1:227833000-227835200	Weak transcription	Thymus	Thymus
41	chr1:227833400-227849600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
42	chr1:227833600-227835200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr1:227833600-227835200	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr1:227833600-227837200	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
45	chr1:227833800-227834400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:227833800-227837600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:227833800-227838800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:227834000-227834400	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
49	chr1:227834000-227834400	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
50	chr1:227834000-227834400	ZNF genes & repeats	Small Intestine	intestine

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