Variant report

Variant	rs2415545
Chromosome Location	chr14:39863802-39863803
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:39863679..39866001-chr14:39899899..39901837,2	MCF-7	breast:
2	chr14:39852325..39854478-chr14:39862389..39864800,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000221645	Chromatin interaction
ENSG00000165355	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10143351	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10145949	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10872920	0.81[ASW][hapmap]
rs11157053	0.81[ASW][hapmap]
rs11621330	0.81[ASW][hapmap]
rs12893829	0.89[CHB][hapmap];0.89[JPT][hapmap];0.81[YRI][hapmap]
rs2415543	0.95[CHB][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4902558	0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap]
rs4902560	0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap]
rs6571923	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs6571932	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7160664	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs718364	0.81[ASW][hapmap];0.81[YRI][hapmap]
rs8006893	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8011173	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8012768	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs8019328	0.87[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[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	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

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39770800-39872400	Weak transcription	Colonic Mucosa	Colon
2	chr14:39818800-39867200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr14:39835400-39872400	Weak transcription	Fetal Muscle Leg	muscle
4	chr14:39836200-39872800	Weak transcription	Esophagus	oesophagus
5	chr14:39836400-39870600	Weak transcription	Gastric	stomach
6	chr14:39840000-39864000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr14:39840000-39867000	Weak transcription	Left Ventricle	heart
8	chr14:39840000-39867400	Weak transcription	Pancreas	Pancrea
9	chr14:39840000-39882600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr14:39840200-39867200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr14:39840600-39864400	Weak transcription	Primary B cells from peripheral blood	blood
12	chr14:39841000-39865800	Weak transcription	Primary B cells from cord blood	blood
13	chr14:39841200-39867000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr14:39846200-39864800	Weak transcription	NHEK	skin
15	chr14:39846200-39878800	Weak transcription	Right Ventricle	heart
16	chr14:39846400-39864600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr14:39846400-39867200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr14:39846600-39864600	Weak transcription	HepG2	liver
19	chr14:39846600-39864600	Weak transcription	NH-A	brain
20	chr14:39846600-39864800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr14:39846600-39866600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr14:39846800-39872400	Weak transcription	HSMMtube	muscle
23	chr14:39850400-39870800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr14:39851000-39866800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr14:39851200-39866000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr14:39851200-39868600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr14:39851400-39868600	Weak transcription	Brain Hippocampus Middle	brain
28	chr14:39851400-39868600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr14:39851800-39864600	Weak transcription	Fetal Intestine Large	intestine
30	chr14:39852800-39864600	Weak transcription	Dnd41	blood
31	chr14:39853000-39867400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr14:39853000-39867400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr14:39853200-39866200	Weak transcription	GM12878-XiMat	blood
34	chr14:39853200-39867800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr14:39853600-39866200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr14:39853600-39867200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr14:39853600-39874200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr14:39854400-39872600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr14:39855400-39864600	Weak transcription	HUVEC	blood vessel
40	chr14:39855400-39868800	Weak transcription	Aorta	Aorta
41	chr14:39856200-39864800	Weak transcription	Fetal Thymus	thymus
42	chr14:39856200-39867200	Weak transcription	Thymus	Thymus
43	chr14:39857000-39870400	Weak transcription	Brain Germinal Matrix	brain
44	chr14:39858600-39866200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr14:39860000-39867000	Weak transcription	Ovary	ovary
46	chr14:39860200-39882200	Weak transcription	Fetal Heart	heart
47	chr14:39860400-39868600	Weak transcription	A549	lung
48	chr14:39860600-39866000	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr14:39860600-39867200	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr14:39860800-39868400	Weak transcription	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links