Variant report

Variant	rs17099889
Chromosome Location	chr12:64281973-64281974
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DPY19L2-7	chr12:64281159-64282378	NONHSAT029125

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs17099873	0.95[CHD][hapmap]
rs17099879	0.95[CHD][hapmap];0.92[TSI][hapmap];0.80[ASN][1000 genomes]
rs17099886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17099893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17099896	0.88[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4346062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55884087	0.90[ASN][1000 genomes]
rs61933086	0.90[ASN][1000 genomes]
rs61933093	0.83[ASN][1000 genomes]
rs61933094	0.83[ASN][1000 genomes]
rs61937061	0.98[ASN][1000 genomes]
rs73113977	0.90[ASN][1000 genomes]
rs73126651	0.97[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs73315387	0.90[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	nsv1046836	chr12:63392391-64377169	Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	nsv832442	chr12:64228071-64442771	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:64246200-64286400	Weak transcription	Fetal Brain Female	brain
2	chr12:64250200-64287200	Weak transcription	Aorta	Aorta
3	chr12:64256800-64282600	Weak transcription	Gastric	stomach
4	chr12:64258800-64286200	Weak transcription	Fetal Intestine Small	intestine
5	chr12:64263800-64289200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr12:64264000-64282600	Weak transcription	HMEC	breast
7	chr12:64264000-64294400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr12:64264200-64282400	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr12:64269200-64282800	Weak transcription	Ovary	ovary
10	chr12:64271000-64282800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr12:64271200-64282600	Weak transcription	HepG2	liver
12	chr12:64271800-64282400	Weak transcription	Brain Angular Gyrus	brain
13	chr12:64271800-64282800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr12:64272600-64282600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr12:64273200-64282800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:64274800-64282000	Weak transcription	Adipose Nuclei	Adipose
17	chr12:64274800-64292800	Weak transcription	Right Atrium	heart
18	chr12:64275000-64282600	Weak transcription	Fetal Intestine Large	intestine
19	chr12:64275000-64285000	Weak transcription	Right Ventricle	heart
20	chr12:64276800-64284800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr12:64277000-64282600	Weak transcription	Brain Substantia Nigra	brain
22	chr12:64277000-64282600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr12:64277000-64286400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr12:64277000-64291600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr12:64277200-64282400	Weak transcription	HSMMtube	muscle
26	chr12:64277200-64282400	Weak transcription	NHLF	lung
27	chr12:64277200-64282600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr12:64277200-64285000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr12:64277200-64285200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr12:64277200-64286200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr12:64277200-64286400	Weak transcription	Fetal Heart	heart
32	chr12:64277200-64286600	Weak transcription	Fetal Muscle Leg	muscle
33	chr12:64277200-64299400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr12:64277800-64289400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr12:64278600-64289800	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr12:64279400-64282600	Weak transcription	NHEK	skin
37	chr12:64279400-64282800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr12:64279400-64282800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr12:64279600-64291200	Weak transcription	Fetal Stomach	stomach
40	chr12:64279800-64282200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr12:64279800-64282400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr12:64279800-64282600	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr12:64279800-64282800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr12:64279800-64286400	Weak transcription	Brain Germinal Matrix	brain
45	chr12:64280000-64282600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr12:64280200-64282600	Weak transcription	Placenta	Placenta
47	chr12:64280600-64282600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr12:64280600-64282600	Weak transcription	HSMM	muscle
49	chr12:64281000-64282600	Genic enhancers	A549	lung
50	chr12:64281000-64285200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links