Variant report

Variant	rs2620386
Chromosome Location	chr15:42444610-42444611
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr15:42444442-42444726	MCF10A-Er-Src	breast:	n/a	n/a
2	KAP1	chr15:42443917-42444650	HEK293	kidney:	n/a	n/a
3	ZNF263	chr15:42443615-42444623	HEK293-T-REx	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:42444314..42447262-chr15:42447408..42450681,4	K562	blood:
2	chr15:42443129..42444925-chr15:42485873..42487790,2	MCF-7	breast:
3	chr15:42440587..42442217-chr15:42443778..42446321,2	K562	blood:

Variant related genes	Relation type
PLA2G4F	TF binding region
ENSG00000168907	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10220859	0.84[EUR][1000 genomes]
rs12438509	1.00[CEU][hapmap]
rs12440087	1.00[CEU][hapmap]
rs1619030	0.82[CHB][hapmap]
rs1624183	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1659213	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs1659218	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs1659219	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[GIH][hapmap];0.83[TSI][hapmap]
rs1659222	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[GIH][hapmap];0.83[TSI][hapmap]
rs1678985	0.82[CHB][hapmap]
rs1678986	0.82[CHB][hapmap]
rs1678992	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs1678993	0.82[CHB][hapmap]
rs1679009	0.82[CHB][hapmap]
rs1679010	0.82[CHB][hapmap]
rs1679012	0.82[CHB][hapmap]
rs16972770	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs16972776	1.00[CEU][hapmap];0.82[TSI][hapmap];0.90[EUR][1000 genomes]
rs16972887	1.00[CEU][hapmap]
rs16973008	1.00[CEU][hapmap]
rs16973045	1.00[CEU][hapmap]
rs16973060	1.00[CEU][hapmap]
rs1703750	0.82[CHB][hapmap]
rs1703754	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1703755	0.82[CHB][hapmap]
rs1712418	0.82[CHB][hapmap]
rs2918460	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs3743008	1.00[CEU][hapmap]
rs4506867	1.00[CEU][hapmap]
rs4923932	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs4923945	1.00[CEU][hapmap]
rs4924627	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs4924630	1.00[CEU][hapmap]
rs4924672	1.00[CEU][hapmap]
rs4924673	1.00[CEU][hapmap]
rs60486546	0.90[EUR][1000 genomes]
rs60506946	0.93[EUR][1000 genomes]
rs622442	0.82[CHB][hapmap]
rs622714	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs624841	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs633934	0.82[CHB][hapmap]
rs660126	0.82[CHB][hapmap]
rs678778	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs681029	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7086	0.82[CHB][hapmap];0.90[ASN][1000 genomes]
rs7180279	1.00[CEU][hapmap]
rs73403545	0.93[EUR][1000 genomes]
rs73403546	0.93[EUR][1000 genomes]
rs73403548	0.93[EUR][1000 genomes]
rs73403550	0.87[EUR][1000 genomes]
rs74009020	0.93[EUR][1000 genomes]
rs8033080	0.87[ASN][1000 genomes]
rs8036187	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv471683	chr15:42334375-42502982	Enhancers Bivalent Enhancer Genic enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv832985	chr15:42371482-42564966	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv9245	chr15:42441849-42453572	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42436000-42452000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:42439400-42451200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr15:42439400-42451800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr15:42439600-42448600	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr15:42441200-42450600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr15:42441600-42446200	Weak transcription	Duodenum Mucosa	Duodenum
7	chr15:42441800-42451000	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr15:42442600-42445000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr15:42442600-42447000	Enhancers	Esophagus	oesophagus
10	chr15:42442600-42447400	Weak transcription	Spleen	Spleen
11	chr15:42442800-42445000	Enhancers	NHEK	skin
12	chr15:42442800-42445400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr15:42443000-42445000	Enhancers	Right Ventricle	heart
14	chr15:42443000-42445600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr15:42443200-42445000	Enhancers	Brain Anterior Caudate	brain
16	chr15:42443400-42444800	Enhancers	Osteobl	bone
17	chr15:42443400-42445200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr15:42443400-42445400	Enhancers	Fetal Muscle Trunk	muscle
19	chr15:42443400-42447600	Enhancers	Gastric	stomach
20	chr15:42443600-42444800	Enhancers	Fetal Lung	lung
21	chr15:42443600-42444800	Enhancers	Fetal Muscle Leg	muscle
22	chr15:42443600-42445000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr15:42443600-42445000	Enhancers	Brain Hippocampus Middle	brain
24	chr15:42443600-42445000	Enhancers	Fetal Heart	heart
25	chr15:42443600-42445800	Enhancers	Left Ventricle	heart
26	chr15:42443600-42445800	Enhancers	Lung	lung
27	chr15:42443600-42445800	Enhancers	Psoas Muscle	Psoas
28	chr15:42443600-42447000	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr15:42443600-42447600	Enhancers	Colonic Mucosa	Colon
30	chr15:42443800-42444800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr15:42443800-42444800	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr15:42443800-42444800	Enhancers	Brain Substantia Nigra	brain
33	chr15:42443800-42445000	Enhancers	Muscle Satellite Cultured Cells	--
34	chr15:42443800-42445000	Enhancers	Brain Angular Gyrus	brain
35	chr15:42443800-42446400	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr15:42443800-42448000	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr15:42444000-42444800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr15:42444000-42444800	Enhancers	HSMM	muscle
39	chr15:42444000-42445000	Enhancers	Brain Cingulate Gyrus	brain
40	chr15:42444000-42451600	Weak transcription	HUVEC	blood vessel
41	chr15:42444200-42445000	Enhancers	HMEC	breast
42	chr15:42444200-42445400	Enhancers	Right Atrium	heart
43	chr15:42444200-42445800	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr15:42444400-42444800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr15:42444400-42444800	Enhancers	Aorta	Aorta
46	chr15:42444400-42444800	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr15:42444400-42446400	Strong transcription	Fetal Intestine Small	intestine
48	chr15:42444400-42446600	Weak transcription	Fetal Thymus	thymus
49	chr15:42444400-42447000	Weak transcription	Fetal Kidney	kidney
50	chr15:42444400-42450400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links