Variant report

Variant	rs2638287
Chromosome Location	chr12:56913902-56913903
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	FOXA1	chr12:56913892-56914250	A549	lung:	n/a	chr12:56914088-56914100
2	NR3C1	chr12:56913768-56914200	A549	lung:	n/a	chr12:56914041-56914055
3	NR3C1	chr12:56913842-56914219	A549	lung:	n/a	chr12:56914041-56914055
4	STAT3	chr12:56913896-56914734	MCF10A-Er-Src	breast:	n/a	chr12:56914617-56914628 chr12:56914362-56914373 chr12:56914059-56914070
5	FOXP2	chr12:56913883-56914077	PFSK-1	brain:	n/a	n/a
6	FOXA1	chr12:56913823-56914295	A549	lung:	n/a	chr12:56914088-56914100
7	POLR2A	chr12:56913886-56914221	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:56913236..56916197-chr12:57081511..57083245,2	K562	blood:

Variant related genes	Relation type
RBMS2	TF binding region
ENSG00000110958	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1043011	0.94[CEU][hapmap];0.82[JPT][hapmap]
rs12232026	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs2638301	0.91[AMR][1000 genomes]
rs2638315	0.94[CEU][hapmap];0.82[JPT][hapmap]
rs2657879	0.94[CEU][hapmap];0.82[JPT][hapmap]
rs2657880	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs2657896	1.00[CEU][hapmap];0.81[GIH][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2657907	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2694917	0.83[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2694919	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2933235	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3759091	0.80[GIH][hapmap];0.84[JPT][hapmap]
rs7302925	0.82[JPT][hapmap]
rs7304944	0.82[JPT][hapmap]
rs774211	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs774213	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs774215	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs799260	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs799261	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs813497	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043622	chr12:56571476-56974448	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv541500	chr12:56571476-56974448	Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv1052713	chr12:56848036-56917602	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv899106	chr12:56905558-57004668	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2638287	SPRYD4	cis	lymphoblastoid	seeQTL
rs2638287	SPRYD4	Cis_1M	lymphoblastoid	RTeQTL
rs2638287	RBMS2	cis	lymphoblastoid	seeQTL

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56911600-56915200	Enhancers	Primary neutrophils fromperipheralblood	blood
2	chr12:56911600-56915200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:56911800-56914000	Enhancers	HUVEC	blood vessel
4	chr12:56911800-56914800	Enhancers	Osteobl	bone
5	chr12:56911800-56915200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:56911800-56915200	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr12:56912000-56914800	Weak transcription	Fetal Thymus	thymus
8	chr12:56912200-56915800	Weak transcription	Gastric	stomach
9	chr12:56912200-56915800	Weak transcription	Lung	lung
10	chr12:56912400-56914000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr12:56912600-56914000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr12:56912600-56914000	Weak transcription	Primary B cells from cord blood	blood
13	chr12:56912600-56914000	Enhancers	Hela-S3	cervix
14	chr12:56912600-56914000	Weak transcription	HepG2	liver
15	chr12:56912600-56914000	Weak transcription	HSMMtube	muscle
16	chr12:56912600-56914000	Enhancers	Monocytes-CD14+_RO01746	blood
17	chr12:56912600-56914200	Enhancers	Fetal Muscle Leg	muscle
18	chr12:56912600-56915200	Enhancers	NHEK	skin
19	chr12:56912800-56914000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr12:56912800-56914000	Enhancers	A549	lung
21	chr12:56912800-56914200	Weak transcription	Colonic Mucosa	Colon
22	chr12:56912800-56914400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr12:56912800-56914600	Weak transcription	NH-A	brain
24	chr12:56912800-56915600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr12:56912800-56917200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr12:56913000-56914000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr12:56913000-56914000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr12:56913000-56914000	Weak transcription	NHDF-Ad	bronchial
29	chr12:56913000-56914200	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr12:56913200-56914000	Enhancers	Spleen	Spleen
31	chr12:56913200-56914200	Enhancers	Fetal Muscle Trunk	muscle
32	chr12:56913200-56914800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr12:56913200-56915200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr12:56913400-56915000	Enhancers	Primary T cells from cord blood	blood
35	chr12:56913600-56914000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr12:56913600-56914000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr12:56913600-56914600	Enhancers	Muscle Satellite Cultured Cells	--
38	chr12:56913600-56914600	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr12:56913600-56914600	Enhancers	HMEC	breast
40	chr12:56913600-56915200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr12:56913600-56915200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr12:56913600-56915400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr12:56913600-56915400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr12:56913800-56914000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr12:56913800-56914000	Enhancers	Aorta	Aorta
46	chr12:56913800-56914000	Enhancers	Brain Angular Gyrus	brain
47	chr12:56913800-56914000	Enhancers	Rectal Mucosa Donor 29	rectum
48	chr12:56913800-56914200	Enhancers	H9 Cell Line	embryonic stem cell
49	chr12:56913800-56914400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr12:56913800-56914400	Enhancers	NHLF	lung

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