Variant report

Variant	rs17699749
Chromosome Location	chr12:4136945-4136946
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:4107365..4111293-chr12:4136025..4140047,4	MCF-7	breast:

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]
rs17699732	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:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4132800-4137000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:4132800-4137400	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr12:4132800-4138200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr12:4133400-4137200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:4133400-4137200	Enhancers	Placenta	Placenta
6	chr12:4133400-4137800	Enhancers	Fetal Muscle Leg	muscle
7	chr12:4133800-4137200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr12:4134000-4137000	Enhancers	Brain Germinal Matrix	brain
9	chr12:4134000-4137200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr12:4134200-4137000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr12:4134400-4137000	Enhancers	H1 Cell Line	embryonic stem cell
12	chr12:4134400-4137800	Enhancers	Fetal Thymus	thymus
13	chr12:4134600-4138000	Enhancers	Fetal Intestine Large	intestine
14	chr12:4134800-4137800	Enhancers	Duodenum Mucosa	Duodenum
15	chr12:4135000-4139600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr12:4135200-4137800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr12:4135400-4137400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr12:4135400-4139200	Weak transcription	Fetal Stomach	stomach
19	chr12:4135600-4137000	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr12:4135600-4137200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:4135600-4137200	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr12:4135600-4139000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:4135600-4139600	Weak transcription	Fetal Lung	lung
24	chr12:4135800-4137000	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr12:4135800-4137000	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr12:4135800-4138000	Enhancers	Fetal Intestine Small	intestine
27	chr12:4136000-4137000	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr12:4136000-4137800	Enhancers	H9 Cell Line	embryonic stem cell
29	chr12:4136000-4138000	Genic enhancers	HUES6 Cell Line	embryonic stem cell
30	chr12:4136200-4137000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
31	chr12:4136200-4137200	Enhancers	Spleen	Spleen
32	chr12:4136200-4137400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr12:4136200-4137400	Enhancers	Placenta Amnion	Placenta Amnion
34	chr12:4136400-4137000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr12:4136400-4137000	Enhancers	Liver	Liver
36	chr12:4136400-4137000	Enhancers	Lung	lung
37	chr12:4136400-4137000	Flanking Active TSS	HepG2	liver
38	chr12:4136400-4137200	Enhancers	Primary B cells from peripheral blood	blood
39	chr12:4136400-4137200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
40	chr12:4136400-4137200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
41	chr12:4136400-4137200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
42	chr12:4136400-4137200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
43	chr12:4136400-4137200	Enhancers	Esophagus	oesophagus
44	chr12:4136400-4137800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
45	chr12:4136400-4137800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr12:4136400-4138000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
47	chr12:4136600-4137000	Enhancers	Primary B cells from cord blood	blood
48	chr12:4136600-4137000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
49	chr12:4136600-4137000	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr12:4136600-4137000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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