Variant report

Variant	rs1292929
Chromosome Location	chr1:94125506-94125507
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1011903	0.87[CEU][hapmap]
rs11164963	0.87[CEU][hapmap]
rs12084853	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs12568405	1.00[JPT][hapmap]
rs1567791	0.87[CEU][hapmap]
rs1772781	1.00[JPT][hapmap]
rs236266	1.00[JPT][hapmap]
rs236273	0.84[AMR][1000 genomes]
rs236284	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs236285	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs236287	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs236288	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236291	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236292	0.98[ASN][1000 genomes]
rs236295	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs236296	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs236301	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236308	0.90[JPT][hapmap];0.81[AMR][1000 genomes]
rs236312	1.00[JPT][hapmap]
rs236313	1.00[JPT][hapmap]
rs236343	0.89[JPT][hapmap]
rs368888	0.81[AMR][1000 genomes]
rs3767979	0.89[JPT][hapmap]
rs3767991	1.00[JPT][hapmap]
rs399649	1.00[JPT][hapmap]
rs423493	1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs6541387	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6541389	0.89[CEU][hapmap];0.91[ASN][1000 genomes]
rs6656270	0.85[CEU][hapmap]
rs6660740	0.87[CEU][hapmap]
rs6684568	0.87[ASN][1000 genomes]
rs6701871	0.87[ASN][1000 genomes]
rs6702036	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6704479	0.86[CEU][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7519952	0.90[ASN][1000 genomes]
rs798213	1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs955470	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482370	chr1:94000799-94183692	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv2755338	chr1:94059579-94176079	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1292929	GCLM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94100000-94135800	Weak transcription	Fetal Stomach	stomach
2	chr1:94101600-94128800	Weak transcription	Right Ventricle	heart
3	chr1:94102000-94125600	Weak transcription	Fetal Muscle Trunk	muscle
4	chr1:94103800-94135800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:94106400-94126000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr1:94107200-94125600	Weak transcription	Aorta	Aorta
7	chr1:94108600-94130400	Weak transcription	Esophagus	oesophagus
8	chr1:94110800-94127400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:94110800-94128800	Weak transcription	Primary B cells from peripheral blood	blood
10	chr1:94110800-94130200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr1:94111200-94127600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr1:94111600-94126800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:94111800-94127400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr1:94112400-94125800	Strong transcription	Hela-S3	cervix
15	chr1:94112400-94127400	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr1:94114600-94125600	Weak transcription	Brain Substantia Nigra	brain
17	chr1:94115000-94128800	Weak transcription	Left Ventricle	heart
18	chr1:94115000-94132000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:94117400-94127400	Genic enhancers	Muscle Satellite Cultured Cells	--
20	chr1:94117400-94128800	Weak transcription	Spleen	Spleen
21	chr1:94117600-94127600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr1:94117600-94128200	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr1:94118000-94126000	Weak transcription	Stomach Mucosa	stomach
24	chr1:94119600-94128800	Weak transcription	Lung	lung
25	chr1:94119800-94127200	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr1:94119800-94128800	Weak transcription	Gastric	stomach
27	chr1:94120000-94128800	Weak transcription	Right Atrium	heart
28	chr1:94120400-94126000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr1:94120400-94127400	Weak transcription	Brain Hippocampus Middle	brain
30	chr1:94120400-94127400	Weak transcription	Stomach Smooth Muscle	stomach
31	chr1:94120600-94125600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:94120600-94128800	Weak transcription	Psoas Muscle	Psoas
33	chr1:94120800-94125800	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr1:94120800-94126800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr1:94120800-94127000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr1:94121600-94127400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr1:94122600-94127600	Weak transcription	Duodenum Mucosa	Duodenum
38	chr1:94122800-94128000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr1:94123000-94127200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr1:94123200-94126400	Genic enhancers	A549	lung
41	chr1:94123200-94128800	Weak transcription	Pancreas	Pancrea
42	chr1:94123200-94135800	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr1:94123400-94126400	Genic enhancers	HSMM	muscle
44	chr1:94123400-94127400	Weak transcription	HUVEC	blood vessel
45	chr1:94123600-94125600	Genic enhancers	NHDF-Ad	bronchial
46	chr1:94123800-94126000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:94123800-94127600	Weak transcription	GM12878-XiMat	blood
48	chr1:94124000-94126400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:94124200-94126000	Genic enhancers	Osteobl	bone
50	chr1:94124200-94126200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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