Variant report

Variant	rs236287
Chromosome Location	chr1:94134683-94134684
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:94133319..94135815-chr1:94145818..94148739,4	MCF-7	breast:
2	chr1:94134360..94137272-chr1:94311581..94314212,2	MCF-7	breast:
3	chr1:94117141..94121029-chr1:94132853..94136106,3	K562	blood:

Variant related genes	Relation type
ENSG00000137936	Chromatin interaction
ENSG00000260464	Chromatin interaction
ENSG00000211575	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1011903	0.87[CEU][hapmap]
rs11164963	0.87[CEU][hapmap]
rs12057736	0.84[ASN][1000 genomes]
rs12059154	0.84[ASN][1000 genomes]
rs12084853	0.87[CEU][hapmap]
rs12568405	1.00[JPT][hapmap]
rs1292929	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1567791	0.87[CEU][hapmap]
rs236273	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs236284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236285	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236288	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs236291	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs236292	0.88[ASN][1000 genomes]
rs236301	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs236308	0.88[YRI][hapmap];0.84[AMR][1000 genomes]
rs236311	0.82[AMR][1000 genomes]
rs236343	0.88[JPT][hapmap]
rs368888	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs3767979	0.88[JPT][hapmap]
rs423493	0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6541387	0.89[CEU][hapmap];0.86[ASN][1000 genomes]
rs6541389	0.89[CEU][hapmap];0.86[ASN][1000 genomes]
rs6656270	0.85[CEU][hapmap]
rs6657709	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6660740	0.87[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6684568	0.82[ASN][1000 genomes]
rs6694536	0.84[ASN][1000 genomes]
rs6701871	0.82[ASN][1000 genomes]
rs6702036	0.87[CEU][hapmap];0.86[ASN][1000 genomes]
rs6704479	0.86[CEU][hapmap];0.86[JPT][hapmap]
rs7519952	0.90[ASN][1000 genomes]
rs798213	0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs955470	0.86[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
rs236287	GCLM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94100000-94135800	Weak transcription	Fetal Stomach	stomach
2	chr1:94103800-94135800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:94123200-94135800	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr1:94127400-94143800	Genic enhancers	HMEC	breast
5	chr1:94127400-94144000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:94128800-94137800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:94129000-94137000	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr1:94129200-94144800	Weak transcription	GM12878-XiMat	blood
9	chr1:94129400-94137600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr1:94129800-94135000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:94130800-94134800	Weak transcription	Primary B cells from peripheral blood	blood
12	chr1:94130800-94141000	Genic enhancers	HSMM	muscle
13	chr1:94131000-94138000	Weak transcription	Fetal Brain Male	brain
14	chr1:94131200-94134800	Genic enhancers	HUVEC	blood vessel
15	chr1:94131200-94136200	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:94131200-94136200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:94131200-94144000	Genic enhancers	Placenta	Placenta
18	chr1:94131400-94135800	Weak transcription	Aorta	Aorta
19	chr1:94131400-94136400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:94131400-94137000	Genic enhancers	A549	lung
21	chr1:94131400-94140600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:94131600-94136200	Weak transcription	Fetal Lung	lung
23	chr1:94131600-94143800	Genic enhancers	NHEK	skin
24	chr1:94131800-94140400	Genic enhancers	NHDF-Ad	bronchial
25	chr1:94132000-94135000	Genic enhancers	NH-A	brain
26	chr1:94132400-94135000	Weak transcription	Fetal Heart	heart
27	chr1:94132400-94139600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr1:94132600-94135000	Weak transcription	Gastric	stomach
29	chr1:94132600-94135200	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr1:94132600-94135800	Weak transcription	K562	blood
31	chr1:94132800-94134800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:94132800-94134800	Weak transcription	Brain Anterior Caudate	brain
33	chr1:94132800-94134800	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr1:94132800-94135800	Weak transcription	Duodenum Mucosa	Duodenum
35	chr1:94132800-94137000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:94132800-94137800	Genic enhancers	Muscle Satellite Cultured Cells	--
37	chr1:94132800-94137800	Weak transcription	Pancreas	Pancrea
38	chr1:94132800-94138000	Weak transcription	Fetal Kidney	kidney
39	chr1:94132800-94138600	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr1:94132800-94141000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:94132800-94141800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr1:94132800-94141800	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr1:94132800-94142400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr1:94132800-94142600	Enhancers	Adipose Nuclei	Adipose
45	chr1:94132800-94144600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr1:94133000-94135800	Weak transcription	Spleen	Spleen
47	chr1:94133000-94136400	Enhancers	Stomach Mucosa	stomach
48	chr1:94133000-94137800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr1:94133000-94137800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr1:94133000-94141600	Weak transcription	H1 Cell Line	embryonic stem cell

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