Variant report

Variant	rs4886840
Chromosome Location	chr15:77179002-77179003
allele	A/G
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	POLR2A	chr15:77178966-77179039	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
SCAPER	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10851892	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11072636	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11072637	0.89[ASN][1000 genomes]
rs11635584	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11637296	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12050866	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12903331	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12903586	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12909065	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1567671	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2280194	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2404600	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34450864	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35940181	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3812908	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3812909	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4886506	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4886842	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55817928	0.83[ASN][1000 genomes]
rs56275930	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6495224	0.86[ASN][1000 genomes]
rs907593	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs907594	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9707794	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv542439	chr15:76762161-77196336	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats 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 miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1046137	chr15:76892097-77196336	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv542442	chr15:76892097-77196336	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv3367577	chr15:77015618-77442634	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	esv1803942	chr15:77151005-77210457	Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
8	esv2758388	chr15:77170550-77373448	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	esv2760041	chr15:77170550-77373448	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs4886840	SCAPER	cis	Nerve Tibial	GTEx
rs4886840	SCAPER	cis	Adipose Subcutaneous	GTEx
rs4886840	SCAPER	cis	Whole Blood	GTEx
rs4886840	SCAPER	cis	Artery Tibial	GTEx
rs4886840	SCAPER	cis	Thyroid	GTEx
rs4886840	SCAPER	cis	Esophagus Mucosa	GTEx
rs4886840	ISL2	Cis_1M	lymphoblastoid	RTeQTL
rs4886840	ISL2	cis	Whole Blood	GTEx
rs4886840	SCAPER	cis	Esophagus Muscularis	GTEx
rs4886840	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs4886840	SCAPER	cis	Stomach	GTEx
rs4886840	SCAPER	cis	Skin Sun Exposed Lower leg	GTEx
rs4886840	SCAPER	cis	lung	GTEx

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77112200-77196000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr15:77133200-77196800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr15:77140800-77195800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr15:77142000-77195800	Weak transcription	Right Ventricle	heart
5	chr15:77146400-77196400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr15:77148600-77195600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr15:77148800-77181000	Weak transcription	Fetal Kidney	kidney
8	chr15:77148800-77195600	Weak transcription	Dnd41	blood
9	chr15:77154400-77179600	Weak transcription	Primary hematopoietic stem cells	blood
10	chr15:77158600-77179800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr15:77158600-77180600	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr15:77158600-77190800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr15:77158800-77195600	Weak transcription	Brain Hippocampus Middle	brain
14	chr15:77158800-77195600	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr15:77161400-77188800	Weak transcription	Fetal Heart	heart
16	chr15:77168000-77179600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr15:77168000-77179600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr15:77168400-77179400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr15:77168400-77195000	Weak transcription	Adipose Nuclei	Adipose
20	chr15:77168600-77179600	Weak transcription	Lung	lung
21	chr15:77168600-77180000	Weak transcription	Esophagus	oesophagus
22	chr15:77168600-77180800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr15:77168600-77181600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr15:77168600-77195000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr15:77168600-77195600	Weak transcription	Colon Smooth Muscle	Colon
26	chr15:77168600-77196800	Weak transcription	Pancreas	Pancrea
27	chr15:77168600-77196800	Weak transcription	Spleen	Spleen
28	chr15:77168800-77179200	Weak transcription	Fetal Brain Female	brain
29	chr15:77169400-77179200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr15:77170200-77190600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr15:77172000-77179200	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr15:77172200-77182400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr15:77172800-77195600	Weak transcription	HSMM	muscle
34	chr15:77173400-77179200	Weak transcription	HepG2	liver
35	chr15:77173600-77179800	Weak transcription	Brain Substantia Nigra	brain
36	chr15:77173800-77183600	Weak transcription	Primary T cells from cord blood	blood
37	chr15:77174200-77179600	Weak transcription	Duodenum Mucosa	Duodenum
38	chr15:77175400-77179200	Weak transcription	Fetal Intestine Small	intestine
39	chr15:77175400-77179200	Weak transcription	Thymus	Thymus
40	chr15:77175600-77179600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr15:77175600-77196800	Weak transcription	Aorta	Aorta
42	chr15:77175600-77196800	Weak transcription	Fetal Muscle Trunk	muscle
43	chr15:77175800-77179600	Weak transcription	Fetal Stomach	stomach
44	chr15:77175800-77179600	Weak transcription	Fetal Thymus	thymus
45	chr15:77175800-77195600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr15:77176000-77179600	Weak transcription	Fetal Muscle Leg	muscle
47	chr15:77176000-77190800	Weak transcription	Fetal Intestine Large	intestine
48	chr15:77176000-77191000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr15:77176000-77192800	Weak transcription	Liver	Liver
50	chr15:77176000-77192800	Weak transcription	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links