Variant report

Variant	rs16970319
Chromosome Location	chr15:40367825-40367826
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	chr15:40331393..40333306-chr15:40366048..40367835,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BMF-1	chr15:40367405-40368221	ENSG00000259584.1

Variant related genes	Relation type
ENSG00000248508	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11638521	0.81[ASN][1000 genomes]
rs16970286	0.87[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs16970291	0.94[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs16970305	0.81[JPT][hapmap]
rs16970325	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs28361302	0.88[ASN][1000 genomes]
rs28371998	0.88[ASN][1000 genomes]
rs28379715	0.88[ASN][1000 genomes]
rs28477230	0.86[ASN][1000 genomes]
rs28479712	0.88[ASN][1000 genomes]
rs28537079	0.88[ASN][1000 genomes]
rs28587891	0.93[ASN][1000 genomes]
rs28605815	0.91[ASN][1000 genomes]
rs28620926	0.80[ASN][1000 genomes]
rs4924412	0.80[JPT][hapmap]
rs4924415	0.93[ASN][1000 genomes]
rs4924416	0.93[ASN][1000 genomes]
rs7181230	0.81[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs9972424	0.87[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs9972442	0.85[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	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv428635	chr15:40274500-40436293	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40346200-40372800	Weak transcription	Fetal Kidney	kidney
2	chr15:40359000-40368000	Weak transcription	Ovary	ovary
3	chr15:40361800-40368400	Weak transcription	HMEC	breast
4	chr15:40362200-40368800	Weak transcription	Osteobl	bone
5	chr15:40362200-40372600	Weak transcription	Small Intestine	intestine
6	chr15:40362200-40373000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr15:40362200-40373600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr15:40362400-40368000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr15:40362400-40369200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr15:40362400-40372800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr15:40362400-40374200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:40362600-40370800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr15:40362600-40373800	Weak transcription	Aorta	Aorta
14	chr15:40362800-40372400	Weak transcription	GM12878-XiMat	blood
15	chr15:40364600-40373000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr15:40364800-40376800	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr15:40365000-40368800	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr15:40365000-40373200	Weak transcription	Left Ventricle	heart
19	chr15:40365200-40368000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr15:40365200-40368800	Weak transcription	Placenta	Placenta
21	chr15:40365600-40369000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr15:40365600-40372400	Weak transcription	Fetal Heart	heart
23	chr15:40365600-40374000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr15:40366400-40373000	Weak transcription	Primary B cells from cord blood	blood
25	chr15:40366600-40368200	Enhancers	Pancreas	Pancrea
26	chr15:40366600-40368600	Enhancers	Fetal Thymus	thymus
27	chr15:40366800-40368000	Enhancers	Stomach Mucosa	stomach
28	chr15:40367000-40368200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr15:40367200-40368200	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr15:40367200-40368800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr15:40367200-40369400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr15:40367400-40368000	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr15:40367400-40368000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr15:40367400-40368000	Flanking Active TSS	K562	blood
35	chr15:40367400-40368200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr15:40367400-40368200	Enhancers	Duodenum Mucosa	Duodenum
37	chr15:40367400-40368200	Enhancers	Gastric	stomach
38	chr15:40367400-40368200	Enhancers	Lung	lung
39	chr15:40367400-40368200	Enhancers	HUVEC	blood vessel
40	chr15:40367400-40368200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
41	chr15:40367400-40368600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr15:40367400-40371400	Enhancers	HepG2	liver
43	chr15:40367600-40368000	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr15:40367600-40368000	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr15:40367600-40368000	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr15:40367600-40368000	Enhancers	Adipose Nuclei	Adipose
47	chr15:40367600-40368000	Enhancers	Hela-S3	cervix
48	chr15:40367600-40368200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr15:40367600-40368200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr15:40367600-40368200	Enhancers	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links