Variant report

Variant	rs2340720
Chromosome Location	chr1:161832842-161832843
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:161832356..161834052-chr1:161839680..161841205,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1006310	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10918137	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11581556	0.81[ASN][1000 genomes]
rs12124509	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1847383	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2257107	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2340721	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2499854	0.80[EUR][1000 genomes]
rs3767634	0.81[ASN][1000 genomes]
rs4656336	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61802507	0.81[ASN][1000 genomes]
rs61802510	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6666482	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6683830	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6695760	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7414603	0.82[ASN][1000 genomes]
rs7519514	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7529356	0.81[ASN][1000 genomes]
rs905594	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs931778	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	nsv1014340	chr1:161822791-161852384	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2340720	ATF6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161773400-161854400	Weak transcription	Small Intestine	intestine
2	chr1:161780600-161836600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:161780800-161834000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:161791800-161842000	Weak transcription	Brain Angular Gyrus	brain
5	chr1:161792200-161838000	Weak transcription	Fetal Brain Male	brain
6	chr1:161795200-161860200	Weak transcription	Lung	lung
7	chr1:161795800-161859000	Weak transcription	Pancreas	Pancrea
8	chr1:161805800-161838200	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr1:161805800-161846200	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr1:161808400-161863200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:161808600-161840200	Weak transcription	Right Ventricle	heart
12	chr1:161808800-161858800	Weak transcription	Spleen	Spleen
13	chr1:161809400-161838000	Weak transcription	HMEC	breast
14	chr1:161810600-161835800	Weak transcription	Colonic Mucosa	Colon
15	chr1:161811400-161838400	Strong transcription	Primary B cells from cord blood	blood
16	chr1:161811800-161838200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:161813000-161834200	Weak transcription	Esophagus	oesophagus
18	chr1:161815200-161834600	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr1:161819800-161852600	Weak transcription	NHDF-Ad	bronchial
20	chr1:161820000-161833000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr1:161820600-161849200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr1:161822000-161836000	Weak transcription	HepG2	liver
23	chr1:161822800-161836200	Weak transcription	Aorta	Aorta
24	chr1:161823400-161833000	Weak transcription	Fetal Stomach	stomach
25	chr1:161823400-161833200	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr1:161823600-161839200	Weak transcription	Brain Anterior Caudate	brain
27	chr1:161823600-161842200	Weak transcription	Osteobl	bone
28	chr1:161823600-161858800	Weak transcription	Thymus	Thymus
29	chr1:161823800-161833000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:161823800-161833400	Weak transcription	NHLF	lung
31	chr1:161823800-161857000	Weak transcription	Ovary	ovary
32	chr1:161824000-161835800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr1:161824000-161836000	Weak transcription	Fetal Kidney	kidney
34	chr1:161824000-161838200	Weak transcription	HSMMtube	muscle
35	chr1:161824000-161840400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:161824000-161842400	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr1:161824000-161854400	Weak transcription	NH-A	brain
38	chr1:161824000-161859000	Weak transcription	Brain Cingulate Gyrus	brain
39	chr1:161824200-161836000	Weak transcription	Colon Smooth Muscle	Colon
40	chr1:161824200-161838000	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr1:161824200-161838800	Weak transcription	Fetal Lung	lung
42	chr1:161824200-161841800	Weak transcription	NHEK	skin
43	chr1:161824200-161842200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr1:161824200-161854400	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr1:161824200-161928400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr1:161824400-161853200	Weak transcription	HSMM	muscle
47	chr1:161824400-161882000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr1:161824600-161853400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr1:161824600-161858600	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr1:161824800-161836000	Weak transcription	Fetal Intestine Small	intestine

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