Variant report

Variant	rs12060538
Chromosome Location	chr1:97286381-97286382
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12066944	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12068332	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12068453	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12354003	0.84[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[LWK][hapmap];0.81[MKK][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes]
rs17115756	0.88[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830681	chr1:97165786-97338064	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
2	esv1797391	chr1:97188394-97293023	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
3	esv1801594	chr1:97188394-97293023	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv491816	chr1:97266403-98223619	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:97219000-97291200	Weak transcription	Pancreas	Pancrea
2	chr1:97228600-97289400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:97240600-97292400	Weak transcription	Lung	lung
4	chr1:97254800-97293600	Weak transcription	GM12878-XiMat	blood
5	chr1:97258800-97292200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:97267400-97289400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:97267400-97300800	Weak transcription	Fetal Stomach	stomach
8	chr1:97267800-97291000	Weak transcription	Fetal Intestine Small	intestine
9	chr1:97268400-97286600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:97270400-97293400	Weak transcription	HSMMtube	muscle
11	chr1:97270400-97295800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr1:97270600-97291400	Weak transcription	Left Ventricle	heart
13	chr1:97272000-97286400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr1:97272000-97290600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:97272000-97290800	Weak transcription	Fetal Brain Female	brain
16	chr1:97272200-97301400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr1:97273200-97291600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:97274000-97291200	Weak transcription	Fetal Heart	heart
19	chr1:97278600-97291200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr1:97278800-97292600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr1:97279000-97294400	Weak transcription	Fetal Muscle Trunk	muscle
22	chr1:97279000-97297200	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr1:97279400-97293200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr1:97279400-97299400	Weak transcription	Primary T cells from cord blood	blood
25	chr1:97279400-97303400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:97279600-97289200	Weak transcription	Osteobl	bone
27	chr1:97279800-97286400	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr1:97279800-97294400	Weak transcription	NHEK	skin
29	chr1:97279800-97306000	Weak transcription	Fetal Kidney	kidney
30	chr1:97280000-97289400	Weak transcription	Liver	Liver
31	chr1:97280000-97290200	Weak transcription	Primary hematopoietic stem cells	blood
32	chr1:97280000-97290200	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr1:97280000-97292600	Weak transcription	NH-A	brain
34	chr1:97280400-97287000	Weak transcription	HSMM	muscle
35	chr1:97280400-97291200	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr1:97280600-97289400	Weak transcription	Adipose Nuclei	Adipose
37	chr1:97280600-97292200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr1:97280600-97303400	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr1:97280800-97291800	Weak transcription	Hela-S3	cervix
40	chr1:97281600-97289400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:97281600-97291800	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr1:97281800-97288000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:97281800-97288000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr1:97281800-97288200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr1:97281800-97291000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr1:97281800-97292800	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr1:97281800-97293200	Weak transcription	Thymus	Thymus
48	chr1:97281800-97293600	Weak transcription	Fetal Muscle Leg	muscle
49	chr1:97282000-97291000	Weak transcription	HMEC	breast
50	chr1:97282000-97292400	Weak transcription	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links