Variant report

Variant	rs3923235
Chromosome Location	chr15:40371121-40371122
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:40358638..40360485-chr15:40371045..40374083,3	K562	blood:
2	chr15:40371048..40373362-chr15:40379784..40381665,2	MCF-7	breast:
3	chr15:40370699..40372317-chr15:40379969..40382959,2	MCF-7	breast:
4	chr15:40371046..40373186-chr15:40375916..40377601,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259409	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1010879	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070250	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11631442	1.00[ASN][1000 genomes]
rs12899649	1.00[CHB][hapmap]
rs12912442	1.00[CHB][hapmap]
rs16924528	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17722502	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17722526	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17723133	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2412456	1.00[CHB][hapmap]
rs2412478	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28444847	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28515996	1.00[ASN][1000 genomes]
rs28736699	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28826672	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35781999	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4497657	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924410	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4924413	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924417	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62004114	0.88[EUR][1000 genomes]
rs62004158	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71132133	1.00[ASN][1000 genomes]
rs7181230	0.87[CEU][hapmap]
rs7183977	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs72731415	1.00[ASN][1000 genomes]
rs7497289	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs749748	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8026641	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs937213	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9919974	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9972424	0.87[CEU][hapmap]

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:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40346200-40372800	Weak transcription	Fetal Kidney	kidney
2	chr15:40362200-40372600	Weak transcription	Small Intestine	intestine
3	chr15:40362200-40373000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr15:40362200-40373600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr15:40362400-40372800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr15:40362400-40374200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:40362600-40373800	Weak transcription	Aorta	Aorta
8	chr15:40362800-40372400	Weak transcription	GM12878-XiMat	blood
9	chr15:40364600-40373000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr15:40364800-40376800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr15:40365000-40373200	Weak transcription	Left Ventricle	heart
12	chr15:40365600-40372400	Weak transcription	Fetal Heart	heart
13	chr15:40365600-40374000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr15:40366400-40373000	Weak transcription	Primary B cells from cord blood	blood
15	chr15:40367400-40371400	Enhancers	HepG2	liver
16	chr15:40367800-40373000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr15:40368000-40372800	Weak transcription	Hela-S3	cervix
18	chr15:40368000-40373000	Weak transcription	Stomach Mucosa	stomach
19	chr15:40368000-40373400	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr15:40368200-40371200	Weak transcription	HUVEC	blood vessel
21	chr15:40368200-40372400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr15:40368200-40372800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr15:40368200-40372800	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr15:40368200-40372800	Weak transcription	Duodenum Mucosa	Duodenum
25	chr15:40368200-40372800	Weak transcription	A549	lung
26	chr15:40368200-40372800	Weak transcription	NH-A	brain
27	chr15:40368200-40373000	Weak transcription	Spleen	Spleen
28	chr15:40368200-40373000	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr15:40368200-40373800	Weak transcription	Pancreas	Pancrea
30	chr15:40368200-40374000	Weak transcription	Gastric	stomach
31	chr15:40368400-40372800	Weak transcription	Primary hematopoietic stem cells	blood
32	chr15:40368600-40372400	Weak transcription	K562	blood
33	chr15:40368600-40374000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr15:40368800-40372400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr15:40368800-40372600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr15:40369000-40372400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr15:40369000-40372600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr15:40369400-40372400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr15:40369400-40372400	Weak transcription	Adipose Nuclei	Adipose
40	chr15:40369400-40373000	Weak transcription	Placenta	Placenta
41	chr15:40369400-40373600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr15:40369600-40371400	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr15:40369600-40373000	Weak transcription	Right Atrium	heart
44	chr15:40369600-40373800	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr15:40369800-40372600	Weak transcription	Fetal Intestine Small	intestine
46	chr15:40369800-40373000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr15:40369800-40373000	Weak transcription	Ovary	ovary
48	chr15:40369800-40373000	Weak transcription	HMEC	breast
49	chr15:40370000-40371200	Enhancers	Fetal Thymus	thymus
50	chr15:40370800-40371600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links