Variant report

Variant	rs6693980
Chromosome Location	chr1:161943202-161943203
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	chr1:161934236..161935963-chr1:161941588..161943984,2	K562	blood:
2	chr1:161942432..161944304-chr1:161946800..161948604,2	K562	blood:

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11582286	0.99[ASN][1000 genomes]
rs1962508	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1962509	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2340725	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2340726	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490430	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2490431	0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs4656342	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6427642	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6693833	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9970209	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9970947	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	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
7	nsv548078	chr1:161941219-161980502	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6693980	OR10K1	cis	cerebellum	SCAN
rs6693980	ATF6	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161902800-161943400	Weak transcription	Esophagus	oesophagus
2	chr1:161904800-161956600	Weak transcription	Fetal Brain Male	brain
3	chr1:161927000-161944000	Weak transcription	Colonic Mucosa	Colon
4	chr1:161929000-161943800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:161929200-161944000	Weak transcription	Ovary	ovary
6	chr1:161931200-161943400	Weak transcription	Psoas Muscle	Psoas
7	chr1:161931400-161943400	Weak transcription	K562	blood
8	chr1:161932400-161955400	Weak transcription	Brain Substantia Nigra	brain
9	chr1:161932600-161943800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr1:161932800-161944000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:161933600-161953400	Weak transcription	HSMMtube	muscle
12	chr1:161937400-161944000	Weak transcription	Duodenum Mucosa	Duodenum
13	chr1:161937600-161954800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr1:161938000-161944000	Weak transcription	Liver	Liver
15	chr1:161938000-161944000	Weak transcription	Pancreas	Pancrea
16	chr1:161939200-161946000	Enhancers	Fetal Muscle Leg	muscle
17	chr1:161939200-161956600	Weak transcription	Fetal Intestine Small	intestine
18	chr1:161940600-161944000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:161940800-161944000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:161940800-161944000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:161940800-161952200	Weak transcription	Aorta	Aorta
22	chr1:161942000-161943600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr1:161942000-161944400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
24	chr1:161942200-161943600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:161942200-161945200	Enhancers	Colon Smooth Muscle	Colon
26	chr1:161942200-161945200	Enhancers	Right Ventricle	heart
27	chr1:161942200-161951000	Weak transcription	Lung	lung
28	chr1:161942400-161943400	Enhancers	Spleen	Spleen
29	chr1:161942400-161944000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr1:161942400-161945200	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr1:161942600-161943800	Weak transcription	Fetal Stomach	stomach
32	chr1:161942600-161944400	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr1:161942800-161944000	Enhancers	Gastric	stomach
34	chr1:161942800-161944400	Enhancers	Left Ventricle	heart
35	chr1:161942800-161944400	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr1:161943000-161944800	Enhancers	Rectal Smooth Muscle	rectum
37	chr1:161943000-161951000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr1:161943200-161943400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr1:161943200-161943400	Enhancers	Placenta	Placenta
40	chr1:161943200-161944400	Enhancers	Right Atrium	heart
41	chr1:161943200-161945000	Enhancers	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links