Variant report

Variant	rs2304902
Chromosome Location	chr15:75340727-75340728
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:75333297-75341736	GM12878	blood:	n/a	n/a
2	POU2F2	chr15:75339018-75340835	GM12878	blood:	n/a	n/a
3	POLR2A	chr15:75340536-75341062	GM12878	blood:	n/a	n/a
4	MTA3	chr15:75338784-75340743	GM12878	blood:	n/a	n/a
5	TCF3	chr15:75340681-75341003	GM12878	blood:	n/a	n/a
6	POLR2A	chr15:75338392-75340889	GM12892	blood:	n/a	n/a
7	POLR2A	chr15:75333262-75344076	GM12878	blood:	n/a	n/a
8	JUN	chr15:75338798-75340888	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:75333855..75341122-chr15:75492635..75495814,9	MCF-7	breast:
2	chr15:75338159..75340815-chr15:75340871..75343132,3	MCF-7	breast:
3	chr15:75334694..75336730-chr15:75338711..75340960,2	MCF-7	breast:
4	chr15:75339319..75341137-chr15:75356875..75359232,2	K562	blood:
5	chr15:75338739..75341398-chr15:75344086..75345973,2	MCF-7	breast:
6	chr15:75334055..75342899-chr15:75492444..75498798,20	K562	blood:
7	chr15:75332512..75342228-chr15:75491817..75496419,22	MCF-7	breast:

No data

Variant related genes	Relation type
PPCDC	TF binding region
ENSG00000167173	Chromatin interaction
ENSG00000138621	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11854975	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12101482	0.82[EUR][1000 genomes]
rs12148488	0.80[EUR][1000 genomes]
rs12898551	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12899062	0.81[EUR][1000 genomes]
rs12900072	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12904227	0.80[EUR][1000 genomes]
rs1867148	0.83[EUR][1000 genomes]
rs1867149	0.83[EUR][1000 genomes]
rs35078352	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35116156	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3812945	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4886417	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886648	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4886655	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6495144	0.81[EUR][1000 genomes]
rs7163362	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7163636	0.81[EUR][1000 genomes]
rs7167261	0.81[EUR][1000 genomes]
rs7181261	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8028129	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs8039755	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569993	chr15:75242155-75483752	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	nsv457205	chr15:75336729-75447773	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv569994	chr15:75336729-75447773	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2304902	SCAMP5	cis	Artery Tibial	GTEx
rs2304902	COX5A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75318000-75341400	Weak transcription	Brain Germinal Matrix	brain
2	chr15:75328800-75350400	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr15:75329200-75350400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr15:75329400-75346800	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr15:75333600-75341000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr15:75334000-75344600	Enhancers	Placenta	Placenta
7	chr15:75334200-75344600	Enhancers	Right Ventricle	heart
8	chr15:75334400-75343200	Enhancers	Fetal Heart	heart
9	chr15:75334600-75340800	Enhancers	Fetal Muscle Leg	muscle
10	chr15:75334600-75341000	Enhancers	Lung	lung
11	chr15:75334600-75343200	Enhancers	Right Atrium	heart
12	chr15:75334800-75344600	Enhancers	Left Ventricle	heart
13	chr15:75335200-75344200	Enhancers	Fetal Lung	lung
14	chr15:75336000-75350400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr15:75336600-75343000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr15:75336800-75341200	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr15:75336800-75342400	Enhancers	Brain Cingulate Gyrus	brain
18	chr15:75336800-75342600	Strong transcription	Primary T cells from cord blood	blood
19	chr15:75337200-75353600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr15:75337400-75340800	Enhancers	Spleen	Spleen
21	chr15:75337600-75341000	Weak transcription	Fetal Brain Female	brain
22	chr15:75337800-75341000	Enhancers	Fetal Muscle Trunk	muscle
23	chr15:75338000-75341800	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr15:75338400-75340800	Enhancers	Stomach Mucosa	stomach
25	chr15:75338400-75342000	Genic enhancers	Esophagus	oesophagus
26	chr15:75338400-75342800	Enhancers	Brain Hippocampus Middle	brain
27	chr15:75338600-75340800	Enhancers	Stomach Smooth Muscle	stomach
28	chr15:75338600-75341000	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr15:75338600-75342800	Enhancers	Brain Anterior Caudate	brain
30	chr15:75338600-75343200	Enhancers	Pancreas	Pancrea
31	chr15:75338800-75344000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr15:75339000-75340800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr15:75339000-75340800	Enhancers	HUVEC	blood vessel
34	chr15:75339000-75342800	Enhancers	Ovary	ovary
35	chr15:75339000-75343000	Enhancers	Brain Angular Gyrus	brain
36	chr15:75339200-75342600	Enhancers	Colon Smooth Muscle	Colon
37	chr15:75339400-75342800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr15:75339600-75341600	Weak transcription	Aorta	Aorta
39	chr15:75339600-75342800	Strong transcription	Thymus	Thymus
40	chr15:75339600-75343200	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr15:75339600-75343600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr15:75339600-75344000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr15:75339600-75344400	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr15:75339600-75351800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr15:75339800-75340800	Enhancers	Primary B cells from cord blood	blood
46	chr15:75339800-75342600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr15:75339800-75344000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr15:75339800-75344600	Genic enhancers	Fetal Stomach	stomach
49	chr15:75339800-75346400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr15:75340000-75340800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links