Variant report

Variant	rs1878288
Chromosome Location	chr2:233791390-233791391
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:233790048..233791601-chr2:233794420..233796079,2	K562	blood:
2	chr2:233757939..233760469-chr2:233789148..233791862,2	K562	blood:
3	chr2:233725493..233728211-chr2:233788384..233791443,3	K562	blood:
4	chr2:233757939..233761647-chr2:233789148..233791862,3	K562	blood:

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs2344912	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2675969	0.80[EUR][1000 genomes]
rs778343	0.80[EUR][1000 genomes]
rs778354	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs778356	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs778357	0.80[EUR][1000 genomes]
rs778359	0.80[EUR][1000 genomes]
rs778360	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs895434	0.81[EUR][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	nsv948470	chr2:233166262-233886732	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1005123	chr2:233227729-233920152	Enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv536173	chr2:233227729-233920152	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv834570	chr2:233639160-233805067	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv3377192	chr2:233758324-233835472	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv1014548	chr2:233777859-233816018	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv518226	chr2:233790447-233793517	Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
8	esv3376153	chr2:233791333-233794081	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1878288	TRPM8	cis	cerebellum	SCAN
rs1878288	NGEF	cis	Adipose Subcutaneous	GTEx
rs1878288	SH3BP4	cis	cerebellum	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233781800-233791800	Weak transcription	Pancreas	Pancrea
2	chr2:233784000-233791400	Strong transcription	Liver	Liver
3	chr2:233785000-233792000	Weak transcription	Gastric	stomach
4	chr2:233789200-233791400	Enhancers	Esophagus	oesophagus
5	chr2:233789200-233791600	Strong transcription	HepG2	liver
6	chr2:233789400-233791600	Enhancers	HSMMtube	muscle
7	chr2:233789800-233791400	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
8	chr2:233789800-233791600	Active TSS	Brain Anterior Caudate	brain
9	chr2:233789800-233791600	Bivalent Enhancer	Fetal Intestine Small	intestine
10	chr2:233789800-233791800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
11	chr2:233789800-233791800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:233789800-233792000	Bivalent Enhancer	Fetal Intestine Large	intestine
13	chr2:233789800-233792400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
14	chr2:233789800-233793200	Active TSS	Brain Inferior Temporal Lobe	brain
15	chr2:233790000-233791600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:233790000-233791600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:233790000-233792000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
18	chr2:233790000-233792200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
19	chr2:233790200-233791400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
20	chr2:233790200-233791400	Active TSS	Brain Angular Gyrus	brain
21	chr2:233790200-233791600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
22	chr2:233790200-233791800	Bivalent Enhancer	Fetal Stomach	stomach
23	chr2:233790200-233791800	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
24	chr2:233790200-233792000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr2:233790400-233791400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr2:233790400-233792200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
27	chr2:233790400-233792400	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
28	chr2:233790600-233791400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
29	chr2:233790600-233791800	Bivalent Enhancer	Right Ventricle	heart
30	chr2:233790600-233792400	Bivalent Enhancer	Placenta	Placenta
31	chr2:233790800-233791400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
32	chr2:233790800-233791400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr2:233790800-233791600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:233791000-233791400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr2:233791000-233791400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
36	chr2:233791000-233791600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
37	chr2:233791000-233791600	Bivalent Enhancer	Fetal Lung	lung
38	chr2:233791000-233791800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr2:233791000-233792400	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
40	chr2:233791000-233792400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
41	chr2:233791000-233792600	Bivalent Enhancer	Fetal Brain Male	brain
42	chr2:233791200-233791400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr2:233791200-233791400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr2:233791200-233791400	Bivalent Enhancer	Brain Hippocampus Middle	brain
45	chr2:233791200-233791400	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr2:233791200-233791400	Bivalent Enhancer	Brain Substantia Nigra	brain
47	chr2:233791200-233791400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
48	chr2:233791200-233791600	Bivalent Enhancer	Stomach Smooth Muscle	stomach
49	chr2:233791200-233791800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
50	chr2:233791200-233791800	Bivalent Enhancer	Primary B cells from cord blood	blood

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