Variant report

Variant	rs36178
Chromosome Location	chr3:134647169-134647170
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	chr3:134640278..134641872-chr3:134645739..134647290,2	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10935143	0.80[TSI][hapmap]
rs11707505	0.80[TSI][hapmap]
rs185257	0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs187587	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36160	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs36161	0.85[CEU][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs36165	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36167	0.96[CEU][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36168	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36169	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36171	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs36172	1.00[CEU][hapmap];0.80[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs36174	0.91[JPT][hapmap];0.90[MEX][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs36176	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36177	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36180	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36181	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36182	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36183	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs36184	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36185	0.96[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36186	0.96[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs36187	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs39701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs39702	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs39703	1.00[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];1.00[ASN][1000 genomes]
rs39704	1.00[ASW][hapmap];1.00[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];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]
rs40157	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs40437	1.00[CEU][hapmap];0.80[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs42883	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4955459	0.80[TSI][hapmap]
rs4955520	0.80[TSI][hapmap]
rs4955522	0.80[TSI][hapmap]
rs4955524	0.80[TSI][hapmap]
rs4955528	0.85[EUR][1000 genomes]
rs504033	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs680054	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs972234	0.80[TSI][hapmap]
rs975149	0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs9815290	0.80[TSI][hapmap]
rs9819131	0.81[CEU][hapmap];0.89[EUR][1000 genomes]
rs9825380	0.80[TSI][hapmap]
rs9856814	0.85[TSI][hapmap];0.86[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	nsv1009634	chr3:134543259-134820208	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv536720	chr3:134543259-134820208	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1000277	chr3:134546080-134970837	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	esv10631	chr3:134647088-134648608	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs36178	DNAJC13	cis	parietal	SCAN
rs36178	STAG1	cis	parietal	SCAN
rs36178	EPHB1	cis	multi-tissue	Pritchard

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134639000-134649400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr3:134639400-134653800	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr3:134641600-134650400	Weak transcription	Fetal Brain Male	brain
4	chr3:134641800-134649800	Weak transcription	Brain Anterior Caudate	brain
5	chr3:134642400-134653800	Weak transcription	Brain Germinal Matrix	brain
6	chr3:134644200-134649600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr3:134644200-134654800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:134644600-134656400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:134644800-134649000	Enhancers	Fetal Muscle Leg	muscle
10	chr3:134645200-134647200	Enhancers	HSMMtube	muscle
11	chr3:134645200-134649200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:134646400-134648600	Weak transcription	Fetal Stomach	stomach
13	chr3:134646600-134649600	Enhancers	Fetal Thymus	thymus
14	chr3:134646800-134647200	Genic enhancers	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links