Variant report

Variant	rs134180
Chromosome Location	chr22:28630787-28630788
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:28630686..28633684-chr22:28635655..28637319,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1303845	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs134172	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs134179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs134183	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs134188	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs134196	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.92[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs134489	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs134500	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs134507	1.00[CEU][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap]
rs134526	0.82[EUR][1000 genomes]
rs134541	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap]
rs134543	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs134548	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap]
rs134551	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs138683	0.94[YRI][hapmap]
rs17503350	0.95[CEU][hapmap]
rs2223370	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4822952	0.86[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs5752743	0.85[JPT][hapmap]
rs695591	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs695625	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs715517	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7284814	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8138645	0.81[ASN][1000 genomes]
rs8140229	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.97[AFR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][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	nsv1062877	chr22:28163507-28866350	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv459866	chr22:28540492-28753833	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv588879	chr22:28540492-28753833	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs134180	SUSD2	cis	parietal	SCAN
rs134180	SEC14L4	cis	parietal	SCAN
rs134180	TTC28	cis	cerebellum	SCAN
rs134180	TTC28	cis	lymphoblastoid	seeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28612200-28634800	Weak transcription	Dnd41	blood
2	chr22:28618400-28639600	Weak transcription	Ovary	ovary
3	chr22:28618400-28662200	Weak transcription	Pancreas	Pancrea
4	chr22:28619400-28631000	Weak transcription	Brain Hippocampus Middle	brain
5	chr22:28620400-28639200	Weak transcription	Left Ventricle	heart
6	chr22:28625800-28630800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr22:28626400-28632000	Weak transcription	Aorta	Aorta
8	chr22:28628000-28639400	Weak transcription	Fetal Heart	heart
9	chr22:28628200-28643200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr22:28628600-28630800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr22:28628600-28632800	Weak transcription	HSMMtube	muscle
12	chr22:28628600-28632800	Weak transcription	Osteobl	bone
13	chr22:28628600-28633000	Weak transcription	HSMM	muscle
14	chr22:28628600-28639000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr22:28628600-28640800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr22:28628600-28640800	Weak transcription	NHLF	lung
17	chr22:28630600-28631800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr22:28630600-28633600	Enhancers	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links