Variant report

Variant	rs1004601
Chromosome Location	chr12:106898357-106898358
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10778482	0.84[ASN][1000 genomes]
rs12424092	0.83[ASN][1000 genomes]
rs2244958	0.94[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs2245062	0.80[CHB][hapmap]
rs2250262	0.84[CHB][hapmap]
rs2254755	0.90[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs2264759	0.82[ASN][1000 genomes]
rs2288266	0.85[CHB][hapmap]
rs2288270	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7137444	0.95[CHB][hapmap];0.88[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7137638	0.95[CHB][hapmap];0.88[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs721438	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7303737	0.88[AMR][1000 genomes]
rs7313412	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7315611	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	esv3435035	chr12:106765277-107015325	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv832510	chr12:106787730-106951140	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106828600-106905800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr12:106854400-106904800	Weak transcription	HSMM	muscle
3	chr12:106854600-106899800	Weak transcription	Fetal Thymus	thymus
4	chr12:106856800-106899400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr12:106884800-106899800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr12:106886200-106916400	Weak transcription	A549	lung
7	chr12:106887600-106907800	Weak transcription	Small Intestine	intestine
8	chr12:106887800-106900200	Weak transcription	Fetal Brain Male	brain
9	chr12:106888000-106899800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr12:106888200-106899400	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr12:106888200-106906800	Weak transcription	Brain Substantia Nigra	brain
12	chr12:106888800-106900400	Weak transcription	Colon Smooth Muscle	Colon
13	chr12:106889000-106899600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr12:106889200-106903200	Weak transcription	HMEC	breast
15	chr12:106889200-106904600	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr12:106889200-106905400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr12:106889400-106899600	Strong transcription	Fetal Stomach	stomach
18	chr12:106889400-106904000	Strong transcription	Primary T cells from cord blood	blood
19	chr12:106889400-106904600	Strong transcription	Liver	Liver
20	chr12:106889800-106899600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr12:106889800-106899800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr12:106889800-106900200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:106889800-106901600	Strong transcription	Fetal Muscle Leg	muscle
24	chr12:106890000-106904200	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr12:106890200-106899200	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr12:106890200-106899400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr12:106890400-106899800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr12:106890400-106901400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr12:106890600-106899800	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr12:106890800-106899800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr12:106890800-106905200	Weak transcription	Colonic Mucosa	Colon
32	chr12:106891200-106901600	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr12:106892000-106900000	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr12:106892000-106904400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr12:106892000-106905200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr12:106892000-106906400	Weak transcription	Brain Angular Gyrus	brain
37	chr12:106892000-106907800	Weak transcription	Brain Cingulate Gyrus	brain
38	chr12:106892200-106899400	Weak transcription	HUVEC	blood vessel
39	chr12:106892200-106901200	Weak transcription	Fetal Kidney	kidney
40	chr12:106892400-106899600	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr12:106892400-106905200	Weak transcription	NHEK	skin
42	chr12:106892800-106904000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr12:106892800-106905600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr12:106893000-106899200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr12:106893200-106898600	Strong transcription	Primary B cells from cord blood	blood
46	chr12:106893600-106899600	Strong transcription	Skeletal Muscle Male	skeletal muscle
47	chr12:106893800-106899200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr12:106894400-106916400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr12:106894600-106905200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr12:106894600-106913200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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