Variant report

Variant	rs6670721
Chromosome Location	chr1:160536561-160536562
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:160536541..160539373-chr1:160549161..160552042,2	K562	blood:
2	chr1:160509589..160511505-chr1:160535117..160536932,2	K562	blood:
3	chr1:160521084..160523233-chr1:160536516..160538024,2	K562	blood:
4	chr1:160536235..160543058-chr1:160543478..160548021,8	K562	blood:

Variant related genes	Relation type
ENSG00000066294	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1055880	0.95[CEU][hapmap];0.87[GIH][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs1061217	0.83[CEU][hapmap]
rs11265442	0.84[CEU][hapmap]
rs11265452	0.91[CEU][hapmap];0.86[MEX][hapmap]
rs11583402	0.95[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11585738	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11590035	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]
rs12144628	0.84[CEU][hapmap]
rs12402879	0.84[CEU][hapmap]
rs12728784	0.87[CEU][hapmap]
rs1394078	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs151607	0.83[CEU][hapmap]
rs1572382	0.84[CEU][hapmap]
rs16832283	0.91[CEU][hapmap];0.86[MEX][hapmap]
rs1726	0.82[EUR][1000 genomes]
rs17381453	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17385337	0.87[CEU][hapmap]
rs17385407	0.96[CEU][hapmap]
rs17385878	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1809963	0.91[CEU][hapmap]
rs1998651	0.84[CEU][hapmap]
rs2025516	0.81[CEU][hapmap]
rs2083128	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs2099604	0.91[CEU][hapmap]
rs2753260	0.83[CEU][hapmap];0.93[MEX][hapmap]
rs3733264	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3733265	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3733266	0.96[CEU][hapmap];0.87[GIH][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs3753381	0.80[MEX][hapmap]
rs3753383	0.82[MEX][hapmap]
rs3755898	0.87[EUR][1000 genomes]
rs3766384	0.87[EUR][1000 genomes]
rs3766385	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3766387	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs3766388	0.91[CEU][hapmap]
rs3766389	0.96[CEU][hapmap];0.87[GIH][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs3816146	0.88[CEU][hapmap]
rs4145897	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5002947	1.00[CEU][hapmap];0.94[GIH][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs56040770	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61801562	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61801564	0.86[EUR][1000 genomes]
rs61801565	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61801567	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61802603	0.86[ASN][1000 genomes]
rs61802604	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61802605	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61802606	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61802608	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61802610	0.97[ASN][1000 genomes]
rs6662093	0.84[EUR][1000 genomes]
rs6668760	0.84[CEU][hapmap]
rs6687641	0.92[CEU][hapmap];0.97[GIH][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs6692382	0.84[CEU][hapmap]
rs6697596	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6699346	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs67197441	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72708818	0.86[ASN][1000 genomes]
rs72708832	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7418241	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7539982	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7547054	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs7550771	0.83[CEU][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap]
rs912582	0.96[CEU][hapmap]
rs977019	0.84[CEU][hapmap]

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	esv1829614	chr1:160465291-160595000	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv872491	chr1:160470258-160580549	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv831703	chr1:160496124-160643024	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs6670721	ADAMTS4	cis	cerebellum	SCAN
rs6670721	CD84	Cis_1M	lymphoblastoid	RTeQTL
rs6670721	CD84	cis	lymphoblastoid	seeQTL
rs6670721	OLFML2B	cis	parietal	SCAN
rs6670721	ADAMTS4	cis	parietal	SCAN
rs6670721	HCN3	cis	cerebellum	SCAN
rs6670721	ATF6	cis	parietal	SCAN
rs6670721	VANGL2	cis	cerebellum	SCAN
rs6670721	NHLH1	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160523000-160543200	Weak transcription	Gastric	stomach
2	chr1:160529200-160537000	Weak transcription	K562	blood
3	chr1:160531400-160536800	Weak transcription	Dnd41	blood
4	chr1:160533800-160537600	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr1:160534200-160536800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr1:160534200-160537400	Enhancers	Primary T cells from cord blood	blood
7	chr1:160534400-160537400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr1:160534600-160536800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr1:160534600-160537400	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr1:160534600-160538200	Enhancers	Fetal Lung	lung
11	chr1:160534800-160536800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr1:160534800-160537000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr1:160534800-160537800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr1:160535000-160540000	Enhancers	Monocytes-CD14+_RO01746	blood
15	chr1:160535200-160542200	Enhancers	Fetal Thymus	thymus
16	chr1:160535400-160536800	Weak transcription	GM12878-XiMat	blood
17	chr1:160535400-160537000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr1:160535400-160537200	Weak transcription	Primary B cells from peripheral blood	blood
19	chr1:160535400-160537200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr1:160535400-160542600	Weak transcription	Pancreas	Pancrea
21	chr1:160535400-160547600	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr1:160535600-160536800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr1:160535600-160536800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr1:160535600-160537800	Enhancers	Primary T cells fromperipheralblood	blood
25	chr1:160535800-160537800	Enhancers	Thymus	Thymus
26	chr1:160535800-160538000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr1:160536000-160537000	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr1:160536000-160537600	Weak transcription	Primary B cells from cord blood	blood
29	chr1:160536000-160537600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr1:160536000-160547000	Weak transcription	Adipose Nuclei	Adipose
31	chr1:160536400-160537400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr1:160536400-160538800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood

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