Variant report

Variant	rs510987
Chromosome Location	chr6:27847517-27847518
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs149878	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs149897	0.86[CEU][hapmap];0.85[GIH][hapmap]
rs149942	0.86[CEU][hapmap];0.85[GIH][hapmap]
rs149944	0.86[CEU][hapmap]
rs149945	0.86[CEU][hapmap]
rs149955	0.86[CEU][hapmap]
rs149959	0.86[CEU][hapmap]
rs149972	0.86[CEU][hapmap]
rs149989	0.86[CEU][hapmap]
rs156739	0.86[CEU][hapmap]
rs200951	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs200967	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs200971	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs200988	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs200994	0.82[CEU][hapmap];0.86[TSI][hapmap]
rs200997	0.83[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.92[LWK][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs203876	0.86[CEU][hapmap]
rs9295747	0.81[CHD][hapmap];0.86[LWK][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	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	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
3	nsv1017440	chr6:27734824-27864277	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	370 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	nsv965700	chr6:27845514-27848765	Enhancers Weak transcription Active TSS	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs510987	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs510987	ZNF323	cis	cerebellum	SCAN
rs510987	ZNF192	cis	cerebellum	SCAN
rs510987	ZNF187	cis	cerebellum	SCAN
rs510987	ZKSCAN3	cis	parietal	SCAN
rs510987	HIST1H3C	cis	cerebellum	SCAN
rs510987	NRSN1	cis	cerebellum	SCAN
rs510987	OR2B6	cis	parietal	SCAN
rs510987	BTN2A1	cis	parietal	SCAN
rs510987	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs510987	ZKSCAN3	cis	cerebellum	SCAN
rs510987	ZNF323	cis	parietal	SCAN
rs510987	ZSCAN23	cis	cerebellum	SCAN
rs510987	AL022393.7	cis	Muscle Skeletal	GTEx
rs510987	ZNF204P	cis	parietal	SCAN
rs510987	AL022393.7	cis	Nerve Tibial	GTEx
rs510987	LRRC16A	cis	parietal	SCAN
rs510987	ZNF192	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27842200-27857000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr6:27842400-27850600	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr6:27842600-27855600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:27842800-27855600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr6:27843200-27849200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:27846800-27850000	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr6:27847000-27847800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr6:27847000-27848200	Enhancers	K562	blood
9	chr6:27847200-27848000	Enhancers	Dnd41	blood
10	chr6:27847200-27848200	Enhancers	Fetal Thymus	thymus
11	chr6:27847400-27847800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

what's new

Quick links