Variant report

Variant	rs6683830
Chromosome Location	chr1:161860512-161860513
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:161860318-161861505	K562	blood:	n/a	n/a
2	POLR2A	chr1:161860351-161861179	Hela-S3	cervix:	n/a	n/a
3	E2F6	chr1:161860329-161860595	H1-hESC	embryonic stem cell:	n/a	chr1:161860464-161860475 chr1:161860464-161860475
4	POLR2A	chr1:161860231-161860520	K562	blood:	n/a	n/a
5	E2F6	chr1:161860184-161860917	H1-hESC	embryonic stem cell:	n/a	chr1:161860464-161860475 chr1:161860464-161860475

Variant related genes	Relation type
ENSG00000229808	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1006310	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1027700	0.80[ASN][1000 genomes]
rs1058405	0.80[ASN][1000 genomes]
rs10918137	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10918243	0.80[ASN][1000 genomes]
rs11581556	0.82[ASN][1000 genomes]
rs11590304	0.81[ASN][1000 genomes]
rs12124509	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1847383	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2257107	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2340720	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2340721	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2499854	0.80[EUR][1000 genomes]
rs3767634	0.82[ASN][1000 genomes]
rs4656336	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4657121	0.83[ASN][1000 genomes]
rs61802507	0.82[ASN][1000 genomes]
rs61802510	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6666482	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6695760	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7414603	0.83[ASN][1000 genomes]
rs7519514	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7529356	0.82[ASN][1000 genomes]
rs905594	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs931778	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428257	chr1:161406315-161868263	Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv33393	chr1:161478681-162080327	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv464184	chr1:161646807-161885352	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv548075	chr1:161646807-161885352	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv464206	chr1:161798239-162067447	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv470744	chr1:161798239-162067447	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv548077	chr1:161798239-162067447	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6683830	ATF6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161808400-161863200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr1:161824200-161928400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr1:161824400-161882000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr1:161825600-161863200	Weak transcription	Fetal Heart	heart
5	chr1:161834400-161863200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr1:161836600-161868000	Weak transcription	Fetal Kidney	kidney
7	chr1:161836600-161888400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr1:161836800-161861000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:161841000-161863000	Weak transcription	HepG2	liver
10	chr1:161842400-161863600	Weak transcription	Brain Angular Gyrus	brain
11	chr1:161843200-161864800	Weak transcription	Brain Substantia Nigra	brain
12	chr1:161854600-161871400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr1:161855000-161860600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr1:161855000-161860600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:161855200-161861000	Weak transcription	Fetal Lung	lung
16	chr1:161855200-161867400	Weak transcription	NHEK	skin
17	chr1:161855400-161860600	Weak transcription	Brain Germinal Matrix	brain
18	chr1:161855400-161860800	Weak transcription	HSMM	muscle
19	chr1:161855400-161861000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:161855400-161879000	Weak transcription	Hela-S3	cervix
21	chr1:161855800-161862200	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr1:161855800-161864400	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr1:161856000-161860800	Weak transcription	NHLF	lung
24	chr1:161856000-161861800	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr1:161856000-161862600	Weak transcription	Colonic Mucosa	Colon
26	chr1:161856000-161863200	Weak transcription	Fetal Brain Female	brain
27	chr1:161856000-161863200	Weak transcription	Osteobl	bone
28	chr1:161856400-161861400	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr1:161856400-161861400	Strong transcription	Adipose Nuclei	Adipose
30	chr1:161856400-161861400	Strong transcription	Fetal Intestine Large	intestine
31	chr1:161856400-161861600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr1:161856400-161861800	Strong transcription	Liver	Liver
33	chr1:161856600-161861000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr1:161856600-161861600	Strong transcription	Primary B cells from cord blood	blood
35	chr1:161856600-161861600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr1:161856800-161861600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:161857200-161860600	Weak transcription	Brain Hippocampus Middle	brain
38	chr1:161857200-161861600	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr1:161857200-161861600	Strong transcription	Dnd41	blood
40	chr1:161857400-161861800	Strong transcription	Primary B cells from peripheral blood	blood
41	chr1:161857600-161862400	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr1:161857600-161863000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:161858000-161862800	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr1:161858200-161860800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr1:161858200-161862000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr1:161858200-161862000	Strong transcription	Primary T cells from cord blood	blood
47	chr1:161858200-161862000	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr1:161858400-161861400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr1:161858600-161861400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr1:161858600-161861400	Strong transcription	Aorta	Aorta

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