Variant report

Variant	rs12037640
Chromosome Location	chr1:225978787-225978788
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225942841..225944602-chr1:225978711..225981243,2	K562	blood:
2	chr1:225964922..225971483-chr1:225977225..225981439,8	K562	blood:
3	chr1:225976942..225979751-chr1:225984143..225986122,2	K562	blood:

Variant related genes	Relation type
ENSG00000143742	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1050033	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12031296	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12042925	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12045030	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12736440	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12737161	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12745281	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12749689	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2671274	0.88[AMR][1000 genomes]
rs3820231	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56866192	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71646745	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71646746	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7539372	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv524126	chr1:225973777-226210653	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225967800-225980200	Weak transcription	Stomach Mucosa	stomach
2	chr1:225968200-225980000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr1:225969800-225983000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:225970200-225979800	Strong transcription	Primary T cells fromperipheralblood	blood
5	chr1:225970200-225983200	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr1:225970600-225980000	Strong transcription	Duodenum Mucosa	Duodenum
7	chr1:225970600-225980600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:225970600-225981800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:225970800-225982200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:225971000-225979200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:225971000-225979200	Strong transcription	Rectal Mucosa Donor 31	rectum
12	chr1:225971200-225978800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:225971200-225979600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:225971200-225979800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:225971200-225980000	Strong transcription	NH-A	brain
16	chr1:225971200-225980000	Strong transcription	Osteobl	bone
17	chr1:225971400-225980000	Strong transcription	Duodenum Smooth Muscle	Duodenum
18	chr1:225971600-225982800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr1:225971800-225980200	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr1:225972400-225980000	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr1:225972800-225979800	Strong transcription	Muscle Satellite Cultured Cells	--
22	chr1:225973000-225980000	Strong transcription	Fetal Lung	lung
23	chr1:225973200-225979800	Strong transcription	A549	lung
24	chr1:225973600-225979400	Strong transcription	HSMM	muscle
25	chr1:225973600-225980000	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr1:225973600-225983400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:225973800-225979000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:225973800-225986000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:225974600-225985600	Weak transcription	Fetal Heart	heart
30	chr1:225975000-225980600	Weak transcription	Psoas Muscle	Psoas
31	chr1:225975000-225997200	Weak transcription	Brain Substantia Nigra	brain
32	chr1:225975000-225997400	Weak transcription	Aorta	Aorta
33	chr1:225975200-225981200	Weak transcription	Fetal Brain Male	brain
34	chr1:225975400-225981800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr1:225975400-225983800	Weak transcription	Pancreas	Pancrea
36	chr1:225975600-225981600	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr1:225975600-225983400	Weak transcription	NHLF	lung
38	chr1:225976000-225984000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr1:225976200-225984400	Weak transcription	HepG2	liver
40	chr1:225976200-225989000	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr1:225976400-225982400	Weak transcription	Brain Hippocampus Middle	brain
42	chr1:225976800-225981000	Weak transcription	Small Intestine	intestine
43	chr1:225977600-225980000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
44	chr1:225978000-225978800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr1:225978000-225979600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr1:225978000-225980000	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr1:225978200-225978800	Strong transcription	Brain Germinal Matrix	brain
48	chr1:225978200-225978800	Strong transcription	K562	blood
49	chr1:225978200-225979000	Strong transcription	HUVEC	blood vessel
50	chr1:225978200-225979200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links