Variant report

Variant	rs3741556
Chromosome Location	chr12:50187060-50187061
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50186306..50187844-chr12:50216014..50218551,2	K562	blood:
2	chr12:50179103..50181940-chr12:50184858..50188069,3	K562	blood:
3	chr12:50185435..50189006-chr12:50189067..50191880,4	MCF-7	breast:
4	chr12:50135277..50138880-chr12:50184463..50187125,3	K562	blood:
5	chr12:50186398..50188769-chr12:50235247..50237745,2	MCF-7	breast:
6	chr12:50183462..50185925-chr12:50186886..50188688,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000186666	Chromatin interaction
ENSG00000167566	Chromatin interaction
ENSG00000139644	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11169158	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11169159	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12305896	0.94[ASN][1000 genomes]
rs12313989	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12316892	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12425872	0.86[EUR][1000 genomes]
rs2603113	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2720288	0.94[ASN][1000 genomes]
rs2720289	0.94[ASN][1000 genomes]
rs72644869	0.86[EUR][1000 genomes]
rs72644870	0.91[ASN][1000 genomes]
rs72644871	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs897055	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	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	chr12:50178800-50191600	Weak transcription	NHDF-Ad	bronchial
8	chr12:50179200-50213600	Weak transcription	Hela-S3	cervix
9	chr12:50179600-50195200	Weak transcription	Fetal Brain Male	brain
10	chr12:50180400-50189000	Weak transcription	NHEK	skin
11	chr12:50181600-50189200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr12:50181600-50190400	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr12:50181800-50188000	Weak transcription	Fetal Intestine Large	intestine
14	chr12:50181800-50190600	Weak transcription	A549	lung
15	chr12:50182000-50189800	Weak transcription	Fetal Lung	lung
16	chr12:50182000-50191400	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr12:50182000-50191800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr12:50182200-50191200	Weak transcription	Primary B cells from peripheral blood	blood
19	chr12:50182200-50191400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr12:50182400-50191000	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr12:50183000-50188800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr12:50183000-50190400	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr12:50183200-50187600	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr12:50183200-50197600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr12:50183200-50200600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr12:50183200-50201400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr12:50183200-50203400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr12:50183400-50187400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr12:50183400-50190600	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr12:50183400-50191600	Strong transcription	HSMMtube	muscle
31	chr12:50183400-50193200	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr12:50183400-50193400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr12:50183400-50193400	Strong transcription	Adipose Nuclei	Adipose
34	chr12:50183400-50197600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr12:50183400-50200000	Strong transcription	Brain Hippocampus Middle	brain
36	chr12:50183400-50200000	Strong transcription	Brain Inferior Temporal Lobe	brain
37	chr12:50183400-50200200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr12:50183400-50200200	Strong transcription	Stomach Smooth Muscle	stomach
39	chr12:50183400-50200600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr12:50183400-50200600	Strong transcription	Fetal Brain Female	brain
41	chr12:50183400-50202200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr12:50183400-50202200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr12:50183400-50202600	Strong transcription	NHLF	lung
44	chr12:50183600-50189000	Weak transcription	Esophagus	oesophagus
45	chr12:50183600-50190400	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr12:50183800-50187200	Strong transcription	Left Ventricle	heart
47	chr12:50183800-50190600	Weak transcription	Colonic Mucosa	Colon
48	chr12:50183800-50199800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr12:50184000-50190400	Weak transcription	Dnd41	blood
50	chr12:50184000-50190600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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