Variant report

Variant	rs17699732
Chromosome Location	chr12:4135422-4135423
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCND2-2	chr12:4135388-4135779	ENSG00000256969
2	lnc-CCND2-2	chr12:4135388-4135824	ENSG00000256969
3	lnc-CCND2-2	chr12:4134129-4136056	NONHSAT025939

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

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10492325	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11829980	0.89[EUR][1000 genomes]
rs11830453	0.89[EUR][1000 genomes]
rs11833630	0.89[EUR][1000 genomes]
rs11836187	0.87[EUR][1000 genomes]
rs17699749	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17836511	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2358592	0.87[EUR][1000 genomes]
rs2532534	0.89[EUR][1000 genomes]
rs2724198	0.92[EUR][1000 genomes]
rs2724209	0.89[EUR][1000 genomes]
rs57157801	0.91[EUR][1000 genomes]
rs7315461	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530520	chr12:3726841-4601757	Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv832316	chr12:3981184-4180381	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv2761723	chr12:4096815-4161871	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv468982	chr12:4108513-4164815	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv557120	chr12:4108513-4164815	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4132800-4136800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:4132800-4137000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:4132800-4137400	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr12:4132800-4138200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:4133000-4136000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr12:4133200-4136400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr12:4133200-4136800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr12:4133400-4137200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr12:4133400-4137200	Enhancers	Placenta	Placenta
10	chr12:4133400-4137800	Enhancers	Fetal Muscle Leg	muscle
11	chr12:4133800-4137200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr12:4134000-4135600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr12:4134000-4135800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr12:4134000-4136000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr12:4134000-4136000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr12:4134000-4136800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:4134000-4136800	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr12:4134000-4137000	Enhancers	Brain Germinal Matrix	brain
19	chr12:4134000-4137200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr12:4134200-4137000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr12:4134400-4135600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr12:4134400-4135600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
23	chr12:4134400-4135600	Enhancers	HMEC	breast
24	chr12:4134400-4136800	Enhancers	Fetal Brain Female	brain
25	chr12:4134400-4137000	Enhancers	H1 Cell Line	embryonic stem cell
26	chr12:4134400-4137800	Enhancers	Fetal Thymus	thymus
27	chr12:4134600-4135600	Enhancers	Fetal Brain Male	brain
28	chr12:4134600-4136400	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr12:4134600-4136600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr12:4134600-4136600	Enhancers	Pancreas	Pancrea
31	chr12:4134600-4138000	Enhancers	Fetal Intestine Large	intestine
32	chr12:4134800-4135600	Enhancers	Fetal Lung	lung
33	chr12:4134800-4136600	Enhancers	Primary T cells from cord blood	blood
34	chr12:4134800-4136600	Enhancers	Fetal Kidney	kidney
35	chr12:4134800-4137800	Enhancers	Duodenum Mucosa	Duodenum
36	chr12:4135000-4135600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
37	chr12:4135000-4135600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr12:4135000-4135800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
39	chr12:4135000-4136000	Flanking Active TSS	HepG2	liver
40	chr12:4135000-4136600	Weak transcription	Small Intestine	intestine
41	chr12:4135000-4139600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr12:4135200-4135600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
43	chr12:4135200-4135600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:4135200-4135800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
45	chr12:4135200-4136400	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr12:4135200-4136400	Weak transcription	Liver	Liver
47	chr12:4135200-4136800	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr12:4135200-4137800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr12:4135400-4135800	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr12:4135400-4135800	Weak transcription	Fetal Intestine Small	intestine

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