Variant report

Variant	rs2290442
Chromosome Location	chr12:50185334-50185335
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:50185305..50186991-chr12:50194287..50197233,2	K562	blood:
2	chr12:50177362..50179959-chr12:50184689..50186718,2	MCF-7	breast:
3	chr12:50183462..50185925-chr12:50186886..50188688,2	MCF-7	breast:
4	chr12:50179103..50181940-chr12:50184858..50188069,3	K562	blood:
5	chr12:50133468..50135867-chr12:50184074..50185842,2	K562	blood:
6	chr12:50184479..50186991-chr12:50194660..50197233,2	K562	blood:
7	chr12:50135277..50138880-chr12:50184463..50187125,3	K562	blood:
8	chr12:50184523..50186730-chr12:50222306..50224521,3	MCF-7	breast:
9	chr12:50183912..50186626-chr12:50222654..50225172,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000167566	Chromatin interaction
ENSG00000139644	Chromatin interaction
ENSG00000258057	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1075366	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1077498	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1077499	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10783320	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10875969	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11169161	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1470909	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2336448	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2603104	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2603107	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2603110	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2603111	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2720296	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2720298	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2954129	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4463912	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4898530	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs729281	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7313400	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7488361	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7977112	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[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	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50170800-50191200	Weak transcription	Brain Substantia Nigra	brain
2	chr12:50172400-50192600	Weak transcription	Duodenum Mucosa	Duodenum
3	chr12:50174400-50209600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:50177800-50203400	Weak transcription	Fetal Kidney	kidney
5	chr12:50178400-50194000	Weak transcription	NH-A	brain
6	chr12:50178400-50195000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr12:50178600-50185600	Weak transcription	Colon Smooth Muscle	Colon
8	chr12:50178800-50191600	Weak transcription	NHDF-Ad	bronchial
9	chr12:50179200-50213600	Weak transcription	Hela-S3	cervix
10	chr12:50179600-50195200	Weak transcription	Fetal Brain Male	brain
11	chr12:50180400-50189000	Weak transcription	NHEK	skin
12	chr12:50181600-50189200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr12:50181600-50190400	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr12:50181800-50188000	Weak transcription	Fetal Intestine Large	intestine
15	chr12:50181800-50190600	Weak transcription	A549	lung
16	chr12:50182000-50189800	Weak transcription	Fetal Lung	lung
17	chr12:50182000-50191400	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr12:50182000-50191800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr12:50182200-50191200	Weak transcription	Primary B cells from peripheral blood	blood
20	chr12:50182200-50191400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr12:50182400-50191000	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr12:50183000-50188800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr12:50183000-50190400	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr12:50183200-50185400	Strong transcription	Placenta	Placenta
25	chr12:50183200-50187600	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr12:50183200-50197600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr12:50183200-50200600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr12:50183200-50201400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr12:50183200-50203400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr12:50183400-50185400	Genic enhancers	HUES6 Cell Line	embryonic stem cell
31	chr12:50183400-50185600	Strong transcription	Osteobl	bone
32	chr12:50183400-50186400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr12:50183400-50186400	Strong transcription	Primary T cells from cord blood	blood
34	chr12:50183400-50187400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr12:50183400-50190600	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr12:50183400-50191600	Strong transcription	HSMMtube	muscle
37	chr12:50183400-50193200	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr12:50183400-50193400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr12:50183400-50193400	Strong transcription	Adipose Nuclei	Adipose
40	chr12:50183400-50197600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr12:50183400-50200000	Strong transcription	Brain Hippocampus Middle	brain
42	chr12:50183400-50200000	Strong transcription	Brain Inferior Temporal Lobe	brain
43	chr12:50183400-50200200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr12:50183400-50200200	Strong transcription	Stomach Smooth Muscle	stomach
45	chr12:50183400-50200600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr12:50183400-50200600	Strong transcription	Fetal Brain Female	brain
47	chr12:50183400-50202200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr12:50183400-50202200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr12:50183400-50202600	Strong transcription	NHLF	lung
50	chr12:50183600-50185400	Genic enhancers	Primary neutrophils fromperipheralblood	blood

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