Variant report

Variant	rs17109235
Chromosome Location	chr14:39898249-39898250
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	chr14:39649512..39652193-chr14:39897469..39900946,3	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1074117	1.00[AMR][1000 genomes]
rs11623676	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17109037	1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[AMR][1000 genomes]
rs17109079	1.00[MEX][hapmap]
rs17109123	0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[AMR][1000 genomes]
rs17109135	1.00[AMR][1000 genomes]
rs17109146	1.00[AMR][1000 genomes]
rs17109165	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17109170	0.89[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17109216	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1950332	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1955715	1.00[AMR][1000 genomes]
rs1955717	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1955723	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1955728	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2057140	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4438203	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4899281	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4899288	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4899299	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4902644	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57704406	1.00[AMR][1000 genomes]
rs59310392	1.00[AMR][1000 genomes]
rs7142121	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7153292	1.00[AMR][1000 genomes]
rs719456	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8005801	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8012131	1.00[AMR][1000 genomes]
rs8016370	1.00[AMR][1000 genomes]
rs926805	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][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	nsv1037183	chr14:39736939-39949233	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv542048	chr14:39736939-39949233	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	esv3523177	chr14:39875036-40128325	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	esv3523178	chr14:39875036-40128325	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv832774	chr14:39897746-40060823	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39864600-39898800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr14:39886600-39900000	Weak transcription	Esophagus	oesophagus
3	chr14:39886600-39900000	Weak transcription	Pancreas	Pancrea
4	chr14:39886800-39899200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr14:39886800-39899600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr14:39887000-39899200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr14:39889600-39898800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr14:39889800-39898800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr14:39891000-39898400	Weak transcription	Fetal Kidney	kidney
10	chr14:39891200-39898800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr14:39891800-39898800	Weak transcription	Aorta	Aorta
12	chr14:39891800-39898800	Weak transcription	Gastric	stomach
13	chr14:39891800-39898800	Weak transcription	Ovary	ovary
14	chr14:39891800-39898800	Weak transcription	Right Ventricle	heart
15	chr14:39891800-39899000	Weak transcription	Fetal Intestine Small	intestine
16	chr14:39891800-39899000	Weak transcription	Small Intestine	intestine
17	chr14:39893000-39899400	Weak transcription	Fetal Intestine Large	intestine
18	chr14:39893600-39898800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr14:39894400-39898800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr14:39894400-39898800	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr14:39894800-39898800	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr14:39895400-39898800	Enhancers	Primary neutrophils fromperipheralblood	blood
23	chr14:39895400-39898800	Enhancers	Dnd41	blood
24	chr14:39895800-39899000	Weak transcription	Spleen	Spleen
25	chr14:39896000-39898400	Weak transcription	NHEK	skin
26	chr14:39896000-39898600	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr14:39896000-39898800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr14:39896000-39898800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr14:39896000-39898800	Weak transcription	NHDF-Ad	bronchial
30	chr14:39896000-39899000	Weak transcription	Placenta	Placenta
31	chr14:39896000-39899800	Weak transcription	HSMM	muscle
32	chr14:39896000-39900000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr14:39896000-39900200	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr14:39896200-39898400	Weak transcription	HMEC	breast
35	chr14:39896200-39898600	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr14:39896200-39898600	Weak transcription	Fetal Lung	lung
37	chr14:39896200-39898800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr14:39896200-39898800	Weak transcription	Fetal Thymus	thymus
39	chr14:39896200-39898800	Weak transcription	Psoas Muscle	Psoas
40	chr14:39896200-39898800	Weak transcription	Thymus	Thymus
41	chr14:39896200-39898800	Weak transcription	HSMMtube	muscle
42	chr14:39896200-39899000	Weak transcription	Right Atrium	heart
43	chr14:39896200-39899200	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr14:39896200-39899200	Weak transcription	Fetal Muscle Leg	muscle
45	chr14:39896400-39898600	Weak transcription	Duodenum Mucosa	Duodenum
46	chr14:39896400-39898800	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr14:39896400-39898800	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr14:39896400-39898800	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr14:39896400-39898800	Weak transcription	Osteobl	bone
50	chr14:39896400-39899600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links