Variant report

Variant	rs3741555
Chromosome Location	chr12:50190653-50190654
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:50188724..50191324-chr12:50196893..50199572,2	K562	blood:

Variant related genes	Relation type
ENSG00000167566	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11169150	0.82[AMR][1000 genomes]
rs11169153	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11169154	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[GIH][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11169155	0.88[AMR][1000 genomes]
rs11169156	0.87[AMR][1000 genomes]
rs11169160	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.83[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11169172	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.87[AMR][1000 genomes]
rs1470907	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1470908	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3741554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813526	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4898531	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4898533	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[AMR][1000 genomes]
rs59429669	0.87[AMR][1000 genomes]
rs7134749	1.00[CEU][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs897059	1.00[CEU][hapmap];0.87[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[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:116 , 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	chr12:50182000-50191400	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr12:50182000-50191800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr12:50182200-50191200	Weak transcription	Primary B cells from peripheral blood	blood
13	chr12:50182200-50191400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr12:50182400-50191000	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr12:50183200-50197600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr12:50183200-50200600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr12:50183200-50201400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr12:50183200-50203400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr12:50183400-50191600	Strong transcription	HSMMtube	muscle
20	chr12:50183400-50193200	Strong transcription	Skeletal Muscle Female	skeletal muscle
21	chr12:50183400-50193400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr12:50183400-50193400	Strong transcription	Adipose Nuclei	Adipose
23	chr12:50183400-50197600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr12:50183400-50200000	Strong transcription	Brain Hippocampus Middle	brain
25	chr12:50183400-50200000	Strong transcription	Brain Inferior Temporal Lobe	brain
26	chr12:50183400-50200200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr12:50183400-50200200	Strong transcription	Stomach Smooth Muscle	stomach
28	chr12:50183400-50200600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr12:50183400-50200600	Strong transcription	Fetal Brain Female	brain
30	chr12:50183400-50202200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr12:50183400-50202200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr12:50183400-50202600	Strong transcription	NHLF	lung
33	chr12:50183800-50199800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr12:50184000-50192800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr12:50184400-50191200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr12:50184400-50193000	Strong transcription	Brain Cingulate Gyrus	brain
37	chr12:50184400-50200000	Strong transcription	Lung	lung
38	chr12:50184400-50200000	Strong transcription	Spleen	Spleen
39	chr12:50184400-50200200	Strong transcription	Brain Germinal Matrix	brain
40	chr12:50184400-50203200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr12:50184600-50191400	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr12:50184600-50193400	Strong transcription	Skeletal Muscle Male	skeletal muscle
43	chr12:50184600-50194000	Strong transcription	Right Ventricle	heart
44	chr12:50184600-50199800	Strong transcription	Brain Anterior Caudate	brain
45	chr12:50184800-50191200	Weak transcription	HUVEC	blood vessel
46	chr12:50184800-50194200	Strong transcription	Fetal Intestine Small	intestine
47	chr12:50184800-50199800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr12:50185000-50202400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr12:50185200-50196400	Weak transcription	Primary hematopoietic stem cells	blood
50	chr12:50185200-50200000	Strong transcription	Gastric	stomach

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