Variant report

Variant	rs2499849
Chromosome Location	chr1:161931628-161931629
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:161922486..161924980-chr1:161928759..161931643,3	K562	blood:
2	chr1:161930299..161933579-chr1:161936760..161939444,3	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10159039	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10733046	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10737517	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10737518	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10753679	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10753685	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10753686	0.94[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10800106	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10800109	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10800137	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10800157	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10918214	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10918215	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10918224	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10918225	0.94[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10918227	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10918279	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10918290	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12096504	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12142836	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12562272	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13401	0.94[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16827987	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2341470	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2341480	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2341481	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2490442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2499845	0.92[ASN][1000 genomes]
rs2499846	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2499847	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2499848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2499850	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2499852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2499854	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4417044	0.84[ASN][1000 genomes]
rs4570397	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4656340	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4657124	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4657125	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4657126	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6656937	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6670429	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6671373	0.84[ASN][1000 genomes]
rs6683712	0.81[ASN][1000 genomes]
rs6695574	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7417576	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7514053	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7514226	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7516104	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7522210	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9283413	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9287066	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9482	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9659616	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv1007108	chr1:161925814-162002917	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv831747	chr1:161926367-162103311	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2499849	ATF6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161861600-161936000	Weak transcription	Fetal Intestine Small	intestine
2	chr1:161897800-161940000	Weak transcription	Brain Germinal Matrix	brain
3	chr1:161901400-161935400	Weak transcription	Fetal Lung	lung
4	chr1:161902800-161943400	Weak transcription	Esophagus	oesophagus
5	chr1:161904800-161956600	Weak transcription	Fetal Brain Male	brain
6	chr1:161906800-161932200	Weak transcription	Stomach Mucosa	stomach
7	chr1:161911000-161937200	Weak transcription	Gastric	stomach
8	chr1:161911600-161939400	Weak transcription	HepG2	liver
9	chr1:161912600-161941600	Weak transcription	Fetal Kidney	kidney
10	chr1:161914000-161932000	Weak transcription	Aorta	Aorta
11	chr1:161916200-161935600	Weak transcription	Fetal Muscle Trunk	muscle
12	chr1:161924200-161932200	Weak transcription	Brain Angular Gyrus	brain
13	chr1:161924400-161931800	Weak transcription	A549	lung
14	chr1:161924600-161932000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr1:161925000-161937600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr1:161925400-161932200	Strong transcription	Primary B cells from peripheral blood	blood
17	chr1:161926200-161939400	Weak transcription	Fetal Heart	heart
18	chr1:161926200-161942200	Weak transcription	Right Ventricle	heart
19	chr1:161926400-161932000	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr1:161926800-161932000	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr1:161926800-161935200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr1:161927000-161933600	Strong transcription	Primary T cells from cord blood	blood
23	chr1:161927000-161944000	Weak transcription	Colonic Mucosa	Colon
24	chr1:161927400-161933800	Strong transcription	Dnd41	blood
25	chr1:161927600-161933800	Strong transcription	Primary hematopoietic stem cells	blood
26	chr1:161927800-161933600	Strong transcription	Liver	Liver
27	chr1:161927800-161937600	Strong transcription	Primary B cells from cord blood	blood
28	chr1:161928200-161938000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr1:161928200-161938800	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr1:161928400-161941800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr1:161928600-161939000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr1:161929000-161931800	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr1:161929000-161943800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr1:161929200-161931800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:161929200-161932000	Weak transcription	Stomach Smooth Muscle	stomach
36	chr1:161929200-161936600	Weak transcription	Thymus	Thymus
37	chr1:161929200-161944000	Weak transcription	Ovary	ovary
38	chr1:161930600-161932000	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr1:161930800-161932000	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr1:161930800-161932000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:161930800-161933000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr1:161931000-161931800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr1:161931000-161931800	Weak transcription	Hela-S3	cervix
44	chr1:161931000-161932000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr1:161931000-161932000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr1:161931000-161932200	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr1:161931000-161932200	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr1:161931000-161932400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr1:161931000-161932400	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr1:161931000-161936600	Weak transcription	Left Ventricle	heart

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