Variant report

Variant	rs17385407
Chromosome Location	chr1:160473286-160473287
allele	G/T
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	GATA2	chr1:160473036-160473305	SH-SY5Y	brain:	n/a	n/a
2	GATA3	chr1:160473090-160473348	T-47D	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000223009	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1055880	1.00[CEU][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes]
rs11265424	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11265442	0.81[CEU][hapmap]
rs11265452	0.96[CEU][hapmap]
rs11577695	0.80[EUR][1000 genomes]
rs11583402	1.00[CEU][hapmap]
rs11585738	1.00[CEU][hapmap];0.82[GIH][hapmap];0.86[TSI][hapmap]
rs11590035	0.96[CEU][hapmap]
rs12144628	0.81[CEU][hapmap]
rs12402879	0.81[CEU][hapmap]
rs12728784	0.83[CEU][hapmap]
rs1394078	1.00[CEU][hapmap]
rs151607	0.88[CEU][hapmap]
rs1572382	0.81[CEU][hapmap]
rs16832283	0.96[CEU][hapmap]
rs17381453	1.00[CEU][hapmap];0.82[GIH][hapmap];0.86[TSI][hapmap]
rs17385337	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1809963	0.96[CEU][hapmap]
rs1998651	0.81[CEU][hapmap]
rs2025517	0.80[CEU][hapmap]
rs2083128	0.87[CEU][hapmap];0.83[JPT][hapmap]
rs2099604	0.86[CEU][hapmap]
rs2753260	0.88[CEU][hapmap]
rs3733264	1.00[CEU][hapmap];0.86[TSI][hapmap]
rs3733265	1.00[CEU][hapmap];0.86[TSI][hapmap]
rs3733266	1.00[CEU][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes]
rs3766385	1.00[CEU][hapmap]
rs3766387	0.95[CEU][hapmap];0.86[CHD][hapmap]
rs3766388	0.96[CEU][hapmap];0.82[JPT][hapmap]
rs3766389	1.00[CEU][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes]
rs3816146	0.84[CEU][hapmap]
rs5002947	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs55917218	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61802603	0.84[EUR][1000 genomes]
rs6668760	0.81[CEU][hapmap]
rs6670721	0.96[CEU][hapmap]
rs6687641	0.88[CEU][hapmap];0.83[JPT][hapmap];0.81[TSI][hapmap]
rs6692382	0.81[CEU][hapmap]
rs6697596	0.82[EUR][1000 genomes]
rs6699346	0.81[EUR][1000 genomes]
rs72708818	0.83[EUR][1000 genomes]
rs7547054	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs7550771	0.88[CEU][hapmap]
rs912582	1.00[CEU][hapmap]
rs977019	0.81[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	esv3409143	chr1:160473211-160473592	ZNF genes & repeats Weak transcription Genic enhancers Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs17385407	CD84	Cis_1M	lymphoblastoid	RTeQTL
rs17385407	ITLN1	cis	brain	seeQTL
rs17385407	PAK4	trans	brain	seeQTL
rs17385407	NRM	trans	brain	seeQTL
rs17385407	SDHC	cis	brain	seeQTL
rs17385407	CBS	trans	brain	seeQTL
rs17385407	LAMB2	trans	brain	seeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160466200-160474200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr1:160468000-160477000	ZNF genes & repeats	GM12878-XiMat	blood
3	chr1:160470800-160475400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
4	chr1:160471200-160475200	Weak transcription	Placenta	Placenta
5	chr1:160471400-160474600	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr1:160471600-160474200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr1:160471600-160474600	Genic enhancers	Primary B cells from peripheral blood	blood
8	chr1:160471600-160474600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr1:160471800-160473800	Genic enhancers	Primary T cells fromperipheralblood	blood
10	chr1:160471800-160474600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr1:160472000-160475200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr1:160472400-160474200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr1:160472600-160473400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr1:160472600-160473800	Enhancers	Thymus	Thymus
15	chr1:160472800-160474600	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr1:160472800-160474800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr1:160472800-160474800	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr1:160473000-160473400	Weak transcription	Primary T cells from cord blood	blood
19	chr1:160473000-160473800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:160473000-160473800	Enhancers	Fetal Thymus	thymus
21	chr1:160473000-160474200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr1:160473200-160473800	Weak transcription	Primary B cells from cord blood	blood
23	chr1:160473200-160474800	Enhancers	Stomach Mucosa	stomach

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