Variant report

Variant	rs16867256
Chromosome Location	chr2:10101468-10101469
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:10091739..10097867-chr2:10098252..10106254,13	K562	blood:

Variant related genes	Relation type
ENSG00000134317	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11884250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11888501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11893694	0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11902268	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11902457	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs16867251	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16867253	1.00[CHB][hapmap]
rs16867254	1.00[CEU][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16867257	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16867261	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16867277	0.93[GIH][hapmap]
rs17364519	0.86[GIH][hapmap]
rs41264185	1.00[ASN][1000 genomes]
rs41264203	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4496316	1.00[ASN][1000 genomes]
rs4613247	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55780001	1.00[ASN][1000 genomes]
rs59658303	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60026782	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60035701	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61221335	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726950	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6730919	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6731160	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6733974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6734239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6735658	1.00[ASN][1000 genomes]
rs6741117	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6744044	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6744047	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6754701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73913930	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7575106	0.93[GIH][hapmap]
rs759342	1.00[CHB][hapmap]
rs7601896	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948591	chr2:9922257-10141191	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	esv1843231	chr2:9979766-10141191	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1011125	chr2:9996740-10293803	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	nsv1011689	chr2:10023891-10293803	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv1002769	chr2:10064511-10157028	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv997334	chr2:10080327-10189279	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16867256	TAF1B	cis	cerebellum	SCAN
rs16867256	CYS1	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10092600-10104200	Weak transcription	Lung	lung
2	chr2:10092600-10112600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:10092600-10113400	Weak transcription	Left Ventricle	heart
4	chr2:10092800-10110600	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr2:10093200-10105600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:10093200-10110600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr2:10093600-10104400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr2:10093600-10112600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:10094800-10104400	Weak transcription	Fetal Intestine Small	intestine
10	chr2:10094800-10110400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr2:10094800-10124400	Weak transcription	Fetal Intestine Large	intestine
12	chr2:10095000-10105400	Weak transcription	Pancreas	Pancrea
13	chr2:10095000-10112600	Weak transcription	Hela-S3	cervix
14	chr2:10095200-10104000	Weak transcription	Gastric	stomach
15	chr2:10096000-10104000	Weak transcription	Esophagus	oesophagus
16	chr2:10099000-10110000	Strong transcription	Placenta	Placenta
17	chr2:10099000-10115400	Strong transcription	Liver	Liver
18	chr2:10100000-10105400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr2:10100600-10101600	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr2:10100600-10101600	Enhancers	K562	blood
21	chr2:10100600-10102200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:10100600-10102200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:10100800-10101600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr2:10100800-10101600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr2:10101000-10101600	Active TSS	Brain Cingulate Gyrus	brain
26	chr2:10101000-10101600	Enhancers	Fetal Brain Male	brain
27	chr2:10101000-10102000	Strong transcription	Dnd41	blood
28	chr2:10101000-10102400	Active TSS	Brain Inferior Temporal Lobe	brain
29	chr2:10101000-10113200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr2:10101000-10117000	Strong transcription	HepG2	liver
31	chr2:10101200-10101600	Strong transcription	Adipose Nuclei	Adipose
32	chr2:10101200-10101600	Enhancers	Brain Angular Gyrus	brain
33	chr2:10101200-10101600	Flanking Active TSS	Fetal Brain Female	brain
34	chr2:10101200-10101600	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr2:10101200-10102200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr2:10101200-10102200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr2:10101200-10106800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr2:10101400-10104000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr2:10101400-10110400	Weak transcription	Fetal Muscle Leg	muscle
40	chr2:10101400-10110400	Weak transcription	Fetal Stomach	stomach
41	chr2:10101400-10144800	Weak transcription	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links