Variant report

Variant	rs16904237
Chromosome Location	chr8:131298985-131298986
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:131296919..131299075-chr8:131308645..131310618,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1417008	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1426102	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1549454	0.87[CHD][hapmap]
rs1556972	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16904209	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16904210	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16904214	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16904215	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16904227	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16904229	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16904230	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16904232	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16904235	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16904236	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16904247	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16904251	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs16904252	0.92[GIH][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes]
rs16904253	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16904257	0.94[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs16904261	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs16904263	0.94[CEU][hapmap];0.97[GIH][hapmap]
rs17210536	0.82[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs2303444	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2305510	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs4363239	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4629915	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs4733774	0.83[CHD][hapmap]
rs7463951	1.00[YRI][hapmap]
rs749126	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[YRI][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	nsv869334	chr8:131025093-131651487	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv915580	chr8:131025093-131667578	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv465810	chr8:131039109-131331012	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv612234	chr8:131039109-131331012	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv533085	chr8:131042781-131755007	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv831461	chr8:131159819-131302900	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv870148	chr8:131206342-131373989	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16904237	ASAP1	cis	Esophagus Muscularis	GTEx
rs16904237	PHF20L1	cis	parietal	SCAN
rs16904237	ASAP1	cis	cerebellum	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:131282400-131314800	Weak transcription	Gastric	stomach
2	chr8:131283800-131299200	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr8:131289000-131299600	Weak transcription	Pancreas	Pancrea
4	chr8:131289400-131300000	Weak transcription	Fetal Brain Female	brain
5	chr8:131289400-131303600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr8:131289400-131304200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr8:131289600-131300200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr8:131289600-131300200	Weak transcription	Fetal Intestine Small	intestine
9	chr8:131290200-131299600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr8:131290200-131302800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr8:131290200-131305400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr8:131290200-131305600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr8:131291800-131300200	Weak transcription	Placenta	Placenta
14	chr8:131291800-131302400	Weak transcription	Left Ventricle	heart
15	chr8:131291800-131305400	Weak transcription	Lung	lung
16	chr8:131292600-131301800	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr8:131292600-131303000	Weak transcription	Adipose Nuclei	Adipose
18	chr8:131292800-131300200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr8:131292800-131302000	Weak transcription	NH-A	brain
20	chr8:131292800-131304800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr8:131293600-131300600	Weak transcription	A549	lung
22	chr8:131293800-131299000	Weak transcription	HepG2	liver
23	chr8:131294000-131300000	Weak transcription	HUVEC	blood vessel
24	chr8:131295200-131300600	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr8:131295200-131302600	Weak transcription	NHDF-Ad	bronchial
26	chr8:131295400-131299800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr8:131295800-131300000	Enhancers	Primary T cells from cord blood	blood
28	chr8:131296000-131299400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr8:131296000-131300200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr8:131296000-131300400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr8:131296200-131299000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr8:131296200-131299600	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr8:131296200-131300000	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr8:131297000-131299400	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr8:131297000-131299400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr8:131297000-131299400	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr8:131297000-131301000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr8:131297000-131302200	Weak transcription	Psoas Muscle	Psoas
39	chr8:131297200-131299600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr8:131297200-131300200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr8:131297200-131300200	Weak transcription	Fetal Heart	heart
42	chr8:131297200-131302200	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr8:131297200-131302400	Weak transcription	Right Atrium	heart
44	chr8:131297200-131302800	Weak transcription	Right Ventricle	heart
45	chr8:131297200-131303600	Weak transcription	Fetal Brain Male	brain
46	chr8:131297200-131304600	Weak transcription	Spleen	Spleen
47	chr8:131297200-131308200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr8:131297400-131299000	Weak transcription	HMEC	breast
49	chr8:131297400-131299200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr8:131297400-131299200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links