Variant report

Variant	rs12138619
Chromosome Location	chr1:179317712-179317713
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179315802..179317742-chr1:179327309..179329268,2	K562	blood:
2	chr1:179311628..179313681-chr1:179315946..179318351,2	K562	blood:
3	chr1:179316253..179318749-chr1:179321719..179323631,3	MCF-7	breast:
4	chr1:179314011..179316743-chr1:179317198..179320043,2	K562	blood:
5	chr1:179315825..179319571-chr1:179319821..179322785,4	K562	blood:

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10494520	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs10753191	0.95[JPT][hapmap]
rs10753192	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10798662	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10798665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs10798670	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10913731	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913732	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10913733	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913734	0.95[JPT][hapmap]
rs10913742	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10913758	0.80[ASN][1000 genomes]
rs10913806	0.88[CHB][hapmap]
rs12022539	0.80[JPT][hapmap]
rs12047160	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12049237	0.81[JPT][hapmap]
rs12073906	0.80[ASN][1000 genomes]
rs12073970	1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12097041	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12117333	0.91[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs12118625	0.80[ASN][1000 genomes]
rs12120123	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12130876	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12131473	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12131475	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12134114	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12138436	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12144580	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12402165	0.81[JPT][hapmap]
rs12405133	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12405321	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs12408349	1.00[CHB][hapmap]
rs12408477	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs12725126	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12740455	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12745772	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs12759446	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1329276	0.87[CHB][hapmap]
rs13306728	0.87[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs13306731	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13374852	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1475798	0.80[JPT][hapmap]
rs16853917	0.81[JPT][hapmap]
rs16853936	0.80[JPT][hapmap]
rs16854009	0.86[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16854229	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2068234	0.80[JPT][hapmap]
rs2152317	0.81[JPT][hapmap]
rs3753524	0.81[JPT][hapmap]
rs3753526	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs4077551	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4077552	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41308413	0.91[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs41310929	0.91[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs41315575	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4133136	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs4394601	0.82[ASN][1000 genomes]
rs59334094	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61824395	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6425537	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6669967	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7523799	0.91[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs931441	0.81[CHB][hapmap]
rs9660720	0.80[ASN][1000 genomes]
rs975025	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[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	nsv1005278	chr1:179197645-179371395	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv1804302	chr1:179315357-179333194	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179264800-179334200	Weak transcription	Colon Smooth Muscle	Colon
2	chr1:179266400-179322800	Weak transcription	Small Intestine	intestine
3	chr1:179292400-179328000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr1:179293000-179322600	Weak transcription	Fetal Heart	heart
5	chr1:179294200-179324600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:179296800-179327800	Weak transcription	Colonic Mucosa	Colon
7	chr1:179297400-179321600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:179298600-179324200	Weak transcription	Thymus	Thymus
9	chr1:179300400-179334600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr1:179300600-179322400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:179301800-179322800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:179303200-179324600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr1:179303400-179322600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:179304200-179320000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:179304200-179324400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:179304200-179324400	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr1:179304200-179324600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:179304200-179325200	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr1:179304400-179318400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr1:179304400-179324400	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr1:179304600-179324200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr1:179305200-179327200	Weak transcription	Right Ventricle	heart
23	chr1:179305600-179334200	Weak transcription	Pancreas	Pancrea
24	chr1:179305800-179322600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr1:179306000-179321000	Strong transcription	Dnd41	blood
26	chr1:179306800-179324600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr1:179307400-179325800	Weak transcription	Esophagus	oesophagus
28	chr1:179307600-179322600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:179307600-179325200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:179307800-179322200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr1:179308000-179321000	Weak transcription	Fetal Brain Male	brain
32	chr1:179308000-179324400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr1:179308400-179322600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr1:179308600-179318000	Strong transcription	Fetal Intestine Large	intestine
35	chr1:179308600-179322000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:179308800-179318000	Strong transcription	Fetal Muscle Leg	muscle
37	chr1:179308800-179320800	Strong transcription	Osteobl	bone
38	chr1:179309800-179326400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr1:179310000-179325200	Strong transcription	Primary T cells from cord blood	blood
40	chr1:179310200-179322000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr1:179310200-179323000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:179310400-179322800	Weak transcription	Aorta	Aorta
43	chr1:179310400-179324400	Strong transcription	Primary B cells from peripheral blood	blood
44	chr1:179311200-179325200	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr1:179311600-179319800	Strong transcription	NHDF-Ad	bronchial
46	chr1:179311600-179320800	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr1:179311600-179326400	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr1:179311800-179321200	Strong transcription	Duodenum Mucosa	Duodenum
49	chr1:179312000-179317800	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr1:179312000-179324200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links