Variant report

Variant	rs12200460
Chromosome Location	chr6:143020804-143020805
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12200517	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13206772	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13212224	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13212849	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[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	nsv949088	chr6:142561402-143128849	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv830828	chr6:142970134-143116517	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:143014400-143023800	Weak transcription	Right Atrium	heart
2	chr6:143014400-143028200	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr6:143014600-143023800	Weak transcription	Left Ventricle	heart
4	chr6:143015000-143023600	Weak transcription	NHEK	skin
5	chr6:143015200-143026600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr6:143016400-143023800	Weak transcription	Spleen	Spleen
7	chr6:143017800-143023600	Weak transcription	Brain Anterior Caudate	brain
8	chr6:143018000-143023400	Weak transcription	HUVEC	blood vessel
9	chr6:143018000-143023600	Weak transcription	Brain Substantia Nigra	brain
10	chr6:143018200-143021800	Weak transcription	HSMMtube	muscle
11	chr6:143018200-143023600	Weak transcription	Lung	lung
12	chr6:143018400-143023800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:143018800-143023800	Weak transcription	Esophagus	oesophagus
14	chr6:143018800-143023800	Weak transcription	Fetal Muscle Trunk	muscle
15	chr6:143018800-143024000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr6:143018800-143029000	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr6:143019000-143023800	Weak transcription	Fetal Thymus	thymus
18	chr6:143019200-143021600	Weak transcription	Psoas Muscle	Psoas
19	chr6:143019200-143021800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr6:143019200-143023600	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr6:143019400-143021800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr6:143019400-143022000	Weak transcription	Primary hematopoietic stem cells	blood
23	chr6:143019400-143023600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr6:143019400-143023600	Weak transcription	Fetal Brain Female	brain
25	chr6:143019400-143023800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr6:143019400-143023800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr6:143019400-143023800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr6:143019400-143023800	Weak transcription	Placenta	Placenta
29	chr6:143019600-143021800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr6:143019600-143022000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr6:143019600-143023600	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr6:143019600-143023600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr6:143019800-143021600	Weak transcription	Fetal Lung	lung
34	chr6:143019800-143021600	Weak transcription	Fetal Muscle Leg	muscle
35	chr6:143019800-143021800	Weak transcription	Fetal Stomach	stomach
36	chr6:143019800-143021800	Weak transcription	Ovary	ovary
37	chr6:143019800-143023600	Weak transcription	Brain Hippocampus Middle	brain
38	chr6:143019800-143023600	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr6:143019800-143023800	Weak transcription	Brain Angular Gyrus	brain
40	chr6:143020000-143021200	Enhancers	Monocytes-CD14+_RO01746	blood
41	chr6:143020000-143023400	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr6:143020000-143023800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr6:143020600-143021200	Enhancers	GM12878-XiMat	blood
44	chr6:143020600-143021400	Weak transcription	Fetal Brain Male	brain
45	chr6:143020600-143022000	Enhancers	Primary B cells from peripheral blood	blood
46	chr6:143020600-143023800	Weak transcription	Brain Cingulate Gyrus	brain
47	chr6:143020800-143023400	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr6:143020800-143023800	Weak transcription	Adipose Nuclei	Adipose
49	chr6:143020800-143024600	Enhancers	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links