Variant report

Variant	rs7550771
Chromosome Location	chr1:160582724-160582725
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:160582022..160584831-chr1:160612719..160614744,2	K562	blood:
2	chr1:160577461..160579543-chr1:160581700..160584306,2	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1055880	0.87[CEU][hapmap];0.83[GIH][hapmap]
rs1061217	0.91[CEU][hapmap]
rs11265442	0.92[CEU][hapmap]
rs11265452	0.92[CEU][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.80[EUR][1000 genomes]
rs11583402	0.91[CEU][hapmap]
rs11585738	0.88[CEU][hapmap];1.00[MEX][hapmap]
rs11590035	0.83[CEU][hapmap]
rs12144628	0.84[CEU][hapmap]
rs12402879	0.92[CEU][hapmap]
rs12728784	0.92[CEU][hapmap]
rs1394078	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1503854	0.85[JPT][hapmap]
rs151607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1572382	0.92[CEU][hapmap]
rs164283	0.81[JPT][hapmap]
rs16832283	0.92[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.82[EUR][1000 genomes]
rs17381453	0.88[CEU][hapmap];1.00[MEX][hapmap]
rs17385407	0.88[CEU][hapmap]
rs17385878	0.85[EUR][1000 genomes]
rs1809963	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1998651	0.92[CEU][hapmap]
rs2025516	0.80[CEU][hapmap]
rs2025517	0.84[CEU][hapmap]
rs2083128	0.91[CEU][hapmap]
rs2099604	0.86[CEU][hapmap]
rs2753260	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3733264	0.88[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap]
rs3733265	0.88[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap]
rs3733266	0.88[CEU][hapmap];0.83[GIH][hapmap]
rs3753381	0.86[MEX][hapmap]
rs3753383	0.89[CHD][hapmap]
rs3766385	0.88[CEU][hapmap]
rs3766387	0.83[CEU][hapmap]
rs3766388	0.92[CEU][hapmap]
rs3766389	0.88[CEU][hapmap];0.83[GIH][hapmap]
rs3816146	0.88[CEU][hapmap]
rs5002947	0.83[CEU][hapmap];0.80[TSI][hapmap]
rs55841347	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56168064	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56367214	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61801562	0.82[EUR][1000 genomes]
rs61801564	0.81[AMR][1000 genomes]
rs61801567	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6662093	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6668760	0.92[CEU][hapmap]
rs6670721	0.83[CEU][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap]
rs6687641	0.92[CEU][hapmap];0.83[TSI][hapmap]
rs6692382	0.92[CEU][hapmap]
rs7547054	0.92[CEU][hapmap]
rs912582	0.88[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs977019	0.92[CEU][hapmap]

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	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
3	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
4	nsv831714	chr1:160581168-160776809	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7550771	ADAMTS4	cis	cerebellum	SCAN
rs7550771	RAB2L	trans	multi-tissue	Pritchard
rs7550771	KCNJ9	cis	parietal	SCAN
rs7550771	CD84	cis	lymphoblastoid	seeQTL
rs7550771	VANGL2	cis	cerebellum	SCAN
rs7550771	SDHC	cis	brain	seeQTL
rs7550771	OLFML2B	cis	parietal	SCAN
rs7550771	SLAMF6	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160575600-160584000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
2	chr1:160576200-160591400	Weak transcription	Spleen	Spleen
3	chr1:160576400-160584800	Genic enhancers	Fetal Thymus	thymus
4	chr1:160576800-160591400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr1:160577000-160584200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:160577000-160590800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr1:160577200-160584400	Genic enhancers	Thymus	Thymus
8	chr1:160577400-160584200	Strong transcription	Primary T cells from cord blood	blood
9	chr1:160577600-160584400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr1:160577800-160583200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
11	chr1:160578000-160587400	Strong transcription	Primary B cells from peripheral blood	blood
12	chr1:160578200-160582800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr1:160579000-160584000	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr1:160579000-160589400	Strong transcription	GM12878-XiMat	blood
15	chr1:160579600-160583200	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr1:160579800-160583200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr1:160579800-160593200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr1:160580000-160582800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr1:160580200-160583400	Strong transcription	Primary B cells from cord blood	blood
20	chr1:160580600-160582800	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr1:160580800-160584200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr1:160581200-160583000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr1:160581200-160583000	Strong transcription	Primary T killer memory cells from peripheral blood	blood
24	chr1:160582200-160591800	Genic enhancers	Primary T helper cells PMA-I stimulated	--

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