Variant report

Variant	rs66839509
Chromosome Location	chr12:104873339-104873340
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104849668..104855401-chr12:104869919..104879346,13	K562	blood:
2	chr12:104849472..104852370-chr12:104873172..104875509,2	K562	blood:
3	chr12:104871756..104873492-chr12:104876935..104879923,2	K562	blood:
4	chr12:104866750..104869514-chr12:104871657..104874435,3	K562	blood:

Variant related genes	Relation type
ENSG00000171310	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10861221	0.92[EUR][1000 genomes]
rs10861222	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10861223	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10861224	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11112069	0.83[ASN][1000 genomes]
rs11112070	0.80[ASN][1000 genomes]
rs11112074	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12300557	0.81[ASN][1000 genomes]
rs12315283	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1922262	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1922263	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4964809	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7299352	0.98[ASN][1000 genomes]
rs7313791	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7973993	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[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	nsv832502	chr12:104833729-104908288	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv832504	chr12:104853331-105028245	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv868	chr12:104858964-104895572	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1042647	chr12:104861494-104888494	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104855400-104874400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr12:104855400-104874800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:104857000-104873600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:104857800-104873600	Weak transcription	A549	lung
5	chr12:104859200-104879800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr12:104863400-104879200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:104865600-104874600	Weak transcription	HMEC	breast
8	chr12:104866600-104882400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr12:104867400-104874400	Weak transcription	Brain Germinal Matrix	brain
10	chr12:104867400-104874400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr12:104867600-104874400	Weak transcription	Stomach Smooth Muscle	stomach
12	chr12:104867600-104876200	Weak transcription	Colonic Mucosa	Colon
13	chr12:104867600-104879400	Weak transcription	Brain Anterior Caudate	brain
14	chr12:104867600-104879600	Weak transcription	Fetal Brain Female	brain
15	chr12:104869200-104874400	Weak transcription	Fetal Stomach	stomach
16	chr12:104869200-104879400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr12:104869200-104899600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr12:104869400-104874400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr12:104870600-104879200	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr12:104871000-104873600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr12:104871000-104879200	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr12:104871400-104873400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr12:104871400-104874800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr12:104871400-104876400	Weak transcription	Brain Hippocampus Middle	brain
25	chr12:104871600-104874000	Flanking Active TSS	K562	blood
26	chr12:104871800-104873400	Enhancers	Placenta	Placenta
27	chr12:104872400-104873600	Flanking Active TSS	GM12878-XiMat	blood
28	chr12:104872400-104873600	Weak transcription	NHEK	skin
29	chr12:104872400-104873800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
30	chr12:104872400-104874000	Transcr. at gene 5' and 3'	Dnd41	blood
31	chr12:104872400-104876200	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr12:104872600-104873800	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr12:104872600-104873800	Enhancers	Spleen	Spleen
34	chr12:104872600-104874000	Enhancers	Thymus	Thymus
35	chr12:104872600-104874200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr12:104872600-104874400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr12:104872600-104874400	Weak transcription	Adipose Nuclei	Adipose
38	chr12:104872600-104874400	Enhancers	Fetal Thymus	thymus
39	chr12:104872600-104874600	Enhancers	Primary T cells fromperipheralblood	blood
40	chr12:104872600-104874600	Weak transcription	NHLF	lung
41	chr12:104872600-104874800	Enhancers	Duodenum Mucosa	Duodenum
42	chr12:104872600-104874800	Weak transcription	Lung	lung
43	chr12:104872600-104875600	Enhancers	HUVEC	blood vessel
44	chr12:104872600-104878400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr12:104872600-104879200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr12:104872600-104879200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr12:104872600-104882400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr12:104872800-104873800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
49	chr12:104872800-104873800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr12:104872800-104873800	Enhancers	Small Intestine	intestine

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