Variant report

Variant	rs10878377
Chromosome Location	chr12:40720004-40720005
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	12:40716064-40722905..12:40793507-40812339	GM12878	blood:

Variant related genes	Relation type
ENSG00000205592	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10467144	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs10467146	0.86[JPT][hapmap]
rs10735931	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs10735934	0.82[JPT][hapmap]
rs10748029	0.82[ASN][1000 genomes]
rs10748030	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs10748033	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs10748034	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs10784486	0.95[CHB][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10784501	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs10784503	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs10784504	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs10784506	0.88[CHB][hapmap];0.84[ASN][1000 genomes]
rs10784509	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs10784548	0.86[JPT][hapmap]
rs10784585	0.86[JPT][hapmap]
rs10878358	0.82[ASN][1000 genomes]
rs10878368	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs10878371	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs10878441	0.86[JPT][hapmap]
rs11176013	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs12426362	0.82[JPT][hapmap]
rs1427263	0.95[CHB][hapmap];0.90[JPT][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1427264	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs1427265	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs1427266	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs1427267	1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1896252	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs1896253	0.90[CHB][hapmap]
rs1896254	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs2069228	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2114568	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs2114569	0.85[CHB][hapmap];0.84[ASN][1000 genomes]
rs2162469	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs2896975	1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3761863	0.86[JPT][hapmap]
rs3886747	0.86[JPT][hapmap]
rs4310676	0.95[CHB][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4483664	0.95[CHB][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4767969	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs4767973	0.86[JPT][hapmap]
rs4768224	0.95[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs4768227	0.84[CHB][hapmap];0.84[ASN][1000 genomes]
rs4768229	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs4768236	0.86[JPT][hapmap]
rs4768237	0.82[JPT][hapmap]
rs7137160	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs7137665	1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs721709	1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs721711	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs721712	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs721713	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs7298930	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs7302503	1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7305344	1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7307276	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs7307562	0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs7308193	0.95[CHB][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7488873	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7957057	0.95[CHB][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7979341	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs963243	0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[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	nsv1044685	chr12:40574460-40771612	Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv832377	chr12:40704881-40855223	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40640600-40727400	Weak transcription	Spleen	Spleen
2	chr12:40640600-40768200	Weak transcription	Pancreas	Pancrea
3	chr12:40656800-40746400	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr12:40674400-40760400	Weak transcription	Lung	lung
5	chr12:40681200-40763000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr12:40684000-40722600	Weak transcription	Colon Smooth Muscle	Colon
7	chr12:40684000-40722600	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr12:40684000-40725000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr12:40687200-40765000	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr12:40695800-40723600	Weak transcription	Brain Angular Gyrus	brain
11	chr12:40699600-40721800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr12:40704400-40723800	Weak transcription	Brain Anterior Caudate	brain
13	chr12:40705600-40722400	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr12:40706800-40722800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr12:40707800-40724400	Strong transcription	Primary B cells from cord blood	blood
16	chr12:40709600-40721400	Weak transcription	Ovary	ovary
17	chr12:40709800-40721600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr12:40709800-40722400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr12:40710000-40721200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr12:40712000-40736600	Weak transcription	Left Ventricle	heart
21	chr12:40712000-40743400	Weak transcription	Aorta	Aorta
22	chr12:40712400-40721800	Weak transcription	Adipose Nuclei	Adipose
23	chr12:40714200-40759200	Weak transcription	Duodenum Mucosa	Duodenum
24	chr12:40716200-40722400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr12:40716800-40761600	Weak transcription	Fetal Kidney	kidney
26	chr12:40717000-40720400	Weak transcription	Primary B cells from peripheral blood	blood
27	chr12:40717800-40724600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr12:40718000-40721800	Weak transcription	Liver	Liver
29	chr12:40719200-40723800	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr12:40719600-40720600	Active TSS	A549	lung
31	chr12:40719600-40735200	Weak transcription	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links