Variant report

Variant	rs6692382
Chromosome Location	chr1:160551592-160551593
allele	A/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	GATA1	chr1:160551358-160552191	PBDE	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:160510071..160512136-chr1:160549726..160552800,3	K562	blood:

Variant related genes	Relation type
CD84	TF binding region

Extended variants
information (count: 72 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1055880	0.80[CEU][hapmap]
rs1061217	1.00[CEU][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10752638	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10797083	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10908789	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10908792	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10908794	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10908796	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11265442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11265443	0.83[ASN][1000 genomes]
rs11265444	0.94[ASN][1000 genomes]
rs11265449	0.81[CHB][hapmap];0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs11265451	0.80[ASN][1000 genomes]
rs11265452	0.84[CEU][hapmap]
rs1138323	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11583402	0.83[CEU][hapmap]
rs11585738	0.81[CEU][hapmap]
rs11590035	0.84[CEU][hapmap]
rs12048466	0.81[CHD][hapmap];0.80[JPT][hapmap];0.80[ASN][1000 genomes]
rs12144628	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12402879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12728784	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12736781	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1394078	0.81[CEU][hapmap]
rs1394079	0.93[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs151607	0.92[CEU][hapmap]
rs1572382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1604783	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16832283	0.84[CEU][hapmap]
rs17381453	0.81[CEU][hapmap]
rs17385407	0.81[CEU][hapmap]
rs1809963	0.84[CEU][hapmap]
rs1998651	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2025516	0.88[CEU][hapmap]
rs2025517	0.84[CEU][hapmap]
rs2083128	0.92[CEU][hapmap]
rs2089088	0.81[CHD][hapmap];0.80[JPT][hapmap];0.80[ASN][1000 genomes]
rs2099604	0.95[CEU][hapmap];0.81[CHB][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2102225	0.80[ASN][1000 genomes]
rs2102226	0.80[ASN][1000 genomes]
rs2369725	0.80[ASN][1000 genomes]
rs2369726	0.80[ASN][1000 genomes]
rs2753260	0.92[CEU][hapmap]
rs349249	0.87[ASN][1000 genomes]
rs3733264	0.81[CEU][hapmap]
rs3733265	0.81[CEU][hapmap]
rs3733266	0.81[CEU][hapmap]
rs3766385	0.81[CEU][hapmap]
rs3766387	0.84[CEU][hapmap]
rs3766388	0.84[CEU][hapmap]
rs3766389	0.81[CEU][hapmap]
rs3816146	0.96[CEU][hapmap];0.87[CHB][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5002947	0.84[CEU][hapmap]
rs6427535	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6656191	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6660233	0.81[CEU][hapmap];0.96[MEX][hapmap]
rs6668760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6670721	0.84[CEU][hapmap]
rs6687641	0.92[CEU][hapmap]
rs7521247	0.80[ASN][1000 genomes]
rs7526815	0.90[ASN][1000 genomes]
rs7528976	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7534679	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7547054	0.92[CEU][hapmap]
rs7550771	0.92[CEU][hapmap]
rs912582	0.80[CEU][hapmap]
rs927202	0.80[JPT][hapmap];0.80[ASN][1000 genomes]
rs977019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][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	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
4	esv1822379	chr1:160545332-160831143	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6692382	ATF6	cis	parietal	SCAN
rs6692382	ADAMTS4	cis	cerebellum	SCAN
rs6692382	ADAMTS4	cis	parietal	SCAN
rs6692382	VANGL2	cis	cerebellum	SCAN
rs6692382	LRP1B	trans	parietal	SCAN
rs6692382	CD84	Cis_1M	lymphoblastoid	RTeQTL
rs6692382	OLFML2B	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160549200-160554600	Weak transcription	Liver	Liver
2	chr1:160549400-160552000	Enhancers	Duodenum Mucosa	Duodenum
3	chr1:160549400-160552400	Enhancers	K562	blood
4	chr1:160549600-160551600	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr1:160549600-160551600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:160549600-160551600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr1:160549600-160552000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr1:160549600-160552000	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr1:160549600-160552000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr1:160549600-160552000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr1:160549600-160552400	Enhancers	Fetal Intestine Small	intestine
12	chr1:160549800-160551600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:160549800-160551800	Enhancers	Primary T cells fromperipheralblood	blood
14	chr1:160549800-160551800	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr1:160549800-160552000	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr1:160549800-160552000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
17	chr1:160550000-160552000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr1:160550200-160552400	Enhancers	Fetal Intestine Large	intestine
19	chr1:160550400-160551600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr1:160550600-160552000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr1:160550800-160552000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr1:160551200-160552000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr1:160551200-160558400	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr1:160551400-160552000	Enhancers	HepG2	liver

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