Variant report

Variant	rs149878
Chromosome Location	chr6:27878738-27878739
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:27877630..27879504-chr6:27883396..27885333,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 24 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs149897	0.91[CEU][hapmap];0.97[GIH][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs149941	0.85[EUR][1000 genomes]
rs149942	0.91[CEU][hapmap];0.97[GIH][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs149944	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs149945	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs149955	0.91[CEU][hapmap]
rs149959	0.91[CEU][hapmap]
rs149972	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs149978	0.85[EUR][1000 genomes]
rs149989	0.91[CEU][hapmap]
rs156734	0.84[EUR][1000 genomes]
rs156739	0.91[CEU][hapmap]
rs183244	0.81[CEU][hapmap]
rs188105	0.91[CEU][hapmap]
rs200951	0.95[CEU][hapmap];0.95[CHB][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.86[LWK][hapmap];0.89[EUR][1000 genomes]
rs200967	0.88[EUR][1000 genomes]
rs200971	0.87[EUR][1000 genomes]
rs200988	0.95[CEU][hapmap];0.95[CHB][hapmap];0.80[GIH][hapmap];0.89[LWK][hapmap];0.85[EUR][1000 genomes]
rs200997	0.95[CHB][hapmap];0.83[LWK][hapmap]
rs203876	0.91[CEU][hapmap]
rs203877	0.91[CEU][hapmap];0.83[GIH][hapmap]
rs203882	0.91[CEU][hapmap]
rs203884	0.91[CEU][hapmap];0.83[GIH][hapmap]
rs203893	0.91[CEU][hapmap];0.83[GIH][hapmap]
rs4141691	0.81[LWK][hapmap]
rs510987	0.89[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.92[LWK][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6910968	0.84[LWK][hapmap]
rs7742858	0.84[LWK][hapmap]
rs7748445	0.81[LWK][hapmap]
rs7755442	0.81[CEU][hapmap]
rs7769416	0.81[LWK][hapmap]

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	nsv432858	chr6:27719375-28011652	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	387 gene(s)	inside rSNPs	diseases
2	nsv1022173	chr6:27734824-27959408	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
3	nsv883512	chr6:27748631-27969004	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
4	nsv601208	chr6:27810626-27969004	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	237 gene(s)	inside rSNPs	diseases
5	nsv1022651	chr6:27864217-28017997	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
6	nsv830619	chr6:27872302-28062544	Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:24)

SNP	Gene	Cis/trans	Tissue	Source
rs149878	LRRC16A	cis	parietal	SCAN
rs149878	AL022393.7	cis	Muscle Skeletal	GTEx
rs149878	NKAPL	cis	parietal	SCAN
rs149878	ZNF187	cis	cerebellum	SCAN
rs149878	OR2B6	cis	parietal	SCAN
rs149878	ZNF192	cis	parietal	SCAN
rs149878	AL022393.7	cis	Artery Tibial	GTEx
rs149878	ZNF323	cis	Cerebellum	GTEx
rs149878	ZKSCAN3	cis	cerebellum	SCAN
rs149878	ZNF323	cis	Brain Pons	GTEx
rs149878	ZNF323	cis	Frontal Cortex	GTEx
rs149878	ZSCAN23	cis	cerebellum	SCAN
rs149878	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs149878	ZNF192	cis	cerebellum	SCAN
rs149878	OR2B8P	cis	Thyroid	GTEx
rs149878	ZNF323	cis	cerebellum	SCAN
rs149878	RP1-265C24.5	cis	Muscle Skeletal	GTEx
rs149878	ZNF204P	cis	parietal	SCAN
rs149878	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs149878	ZKSCAN3	cis	parietal	SCAN
rs149878	AL022393.7	cis	Nerve Tibial	GTEx
rs149878	ZNF323	cis	parietal	SCAN
rs149878	ZNF323	cis	Temporal Cortex	GTEx
rs149878	AL022393.7	cis	Artery Aorta	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27871600-27883200	Weak transcription	Hela-S3	cervix
2	chr6:27876200-27878800	Weak transcription	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links