Variant report

Variant	rs858984
Chromosome Location	chr6:27177361-27177362
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF3	chr6:27177353-27178009	A549	lung:	n/a	n/a
2	MEF2A	chr6:27177354-27177791	GM12878	blood:	n/a	n/a
3	FOXA2	chr6:27177339-27177761	A549	lung:	n/a	n/a
4	HMGN3	chr6:27177293-27177830	K562	blood:	n/a	n/a
5	TEAD4	chr6:27177336-27177868	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:27115172..27117358-chr6:27175477..27177621,2	K562	blood:
2	chr6:27177161..27179137-chr6:27326485..27328754,2	K562	blood:
3	chr6:27113325..27119101-chr6:27172973..27177922,8	K562	blood:

Variant related genes	Relation type
ENSG00000174572	TF binding region
ENSG00000265565	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000204789	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1062834	0.80[EUR][1000 genomes]
rs10946896	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs1102557	1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11758615	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12153912	0.91[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12189835	0.91[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12189964	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12190473	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs12191280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12192049	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs12192502	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs12193820	0.82[CEU][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs12194893	1.00[JPT][hapmap]
rs12195360	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12196084	0.91[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12196889	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12198077	0.91[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12199218	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs12200798	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12200985	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs12201774	0.91[CEU][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs12203728	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs12204768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12205628	0.80[EUR][1000 genomes]
rs12205921	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs12207614	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12209393	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs12209429	0.91[CEU][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs12209456	0.91[CEU][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs12209800	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12210905	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12213361	0.81[EUR][1000 genomes]
rs12214930	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs12215241	1.00[JPT][hapmap]
rs2023467	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3531	0.91[CEU][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs3800305	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800306	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800310	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3922717	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs4541737	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs4636015	0.91[CEU][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs5030955	0.90[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5030958	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67153537	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6902012	0.89[CEU][hapmap]
rs6917419	0.82[CEU][hapmap]
rs6920115	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs6931711	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6938397	0.82[CEU][hapmap]
rs6940638	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs72843609	0.81[EUR][1000 genomes]
rs72843611	0.81[EUR][1000 genomes]
rs72843613	0.81[EUR][1000 genomes]
rs72843615	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72843619	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72843622	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72843629	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72843633	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72843640	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72843641	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72843643	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72843644	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs858985	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]
rs858986	0.91[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs858988	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs858989	1.00[CEU][hapmap];0.85[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];0.95[ASN][1000 genomes]
rs858992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs858993	0.83[ASN][1000 genomes]
rs858995	0.91[CEU][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9348752	0.80[CEU][hapmap]
rs9348756	1.00[JPT][hapmap]
rs9348759	0.81[CEU][hapmap]
rs9368500	0.81[CEU][hapmap]
rs9379970	0.91[CEU][hapmap]
rs9379975	0.81[CEU][hapmap]
rs9393796	0.82[CEU][hapmap]
rs9393802	0.85[CEU][hapmap]
rs9393803	0.91[CEU][hapmap]
rs9467965	0.89[CEU][hapmap]
rs9467971	0.91[CEU][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	nsv1017328	chr6:27177147-27369588	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs858984	BTN3A2	cis	cerebellum	SCAN
rs858984	BTN3A3	cis	cerebellum	SCAN
rs858984	BTN3A1	cis	cerebellum	SCAN
rs858984	ZNF391	cis	cerebellum	SCAN
rs858984	ZNF192	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27174000-27179600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:27174400-27179000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:27174400-27181400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:27176400-27178000	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr6:27176800-27177400	Flanking Active TSS	H9 Cell Line	embryonic stem cell
6	chr6:27176800-27178000	Enhancers	GM12878-XiMat	blood
7	chr6:27177000-27177400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr6:27177000-27181000	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr6:27177200-27177400	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr6:27177200-27177400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:27177200-27177600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
12	chr6:27177200-27177600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr6:27177200-27177600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:27177200-27178000	Flanking Active TSS	K562	blood
15	chr6:27177200-27181200	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr6:27177200-27181400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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