Variant report

Variant	rs1061217
Chromosome Location	chr1:160580015-160580016
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLAMF1-1	chr1:160579609-160580588	NR_104400

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10752638	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10797083	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10908789	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10908792	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10908794	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10908796	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11265442	1.00[CEU][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11265443	0.81[ASN][1000 genomes]
rs11265444	0.91[ASN][1000 genomes]
rs11265449	0.83[JPT][hapmap];0.92[ASN][1000 genomes]
rs11265451	0.89[ASN][1000 genomes]
rs11265452	0.83[CEU][hapmap]
rs1138323	0.84[EUR][1000 genomes]
rs11583402	0.82[CEU][hapmap]
rs11590035	0.83[CEU][hapmap]
rs12048466	0.83[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs12058421	0.82[AFR][1000 genomes]
rs12144628	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs12402879	1.00[CEU][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12728784	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12736781	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1394079	0.80[CHB][hapmap];0.91[JPT][hapmap];0.98[ASN][1000 genomes]
rs151607	0.91[CEU][hapmap]
rs1572382	1.00[CEU][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1604783	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16832283	0.83[CEU][hapmap]
rs1809963	0.83[CEU][hapmap]
rs1998651	1.00[CEU][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2025516	0.87[CEU][hapmap]
rs2025517	0.83[CEU][hapmap]
rs2083128	0.91[CEU][hapmap]
rs2089088	0.83[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs2099604	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs2102225	0.89[ASN][1000 genomes]
rs2102226	0.89[ASN][1000 genomes]
rs2369725	0.89[ASN][1000 genomes]
rs2369726	0.89[ASN][1000 genomes]
rs2753260	0.91[CEU][hapmap]
rs3766387	0.83[CEU][hapmap]
rs3766388	0.83[CEU][hapmap]
rs3816146	0.92[ASW][hapmap];0.96[CEU][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs5002947	0.83[CEU][hapmap]
rs6427535	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668760	1.00[CEU][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6670721	0.83[CEU][hapmap]
rs6687641	0.91[CEU][hapmap]
rs6692382	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]
rs7526815	0.96[ASN][1000 genomes]
rs7534679	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7547054	0.91[CEU][hapmap]
rs7550771	0.91[CEU][hapmap]
rs927202	0.80[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs977019	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1061217	CD84	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:32 , 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	chr1:160576000-160580200	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr1:160576200-160591400	Weak transcription	Spleen	Spleen
4	chr1:160576400-160584800	Genic enhancers	Fetal Thymus	thymus
5	chr1:160576800-160591400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr1:160577000-160580200	Weak transcription	Fetal Intestine Large	intestine
7	chr1:160577000-160580400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr1:160577000-160580800	Weak transcription	Fetal Intestine Small	intestine
9	chr1:160577000-160581000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
10	chr1:160577000-160584200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:160577000-160590800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr1:160577200-160584400	Genic enhancers	Thymus	Thymus
13	chr1:160577400-160584200	Strong transcription	Primary T cells from cord blood	blood
14	chr1:160577600-160580200	Weak transcription	Dnd41	blood
15	chr1:160577600-160580200	Weak transcription	K562	blood
16	chr1:160577600-160580600	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr1:160577600-160584400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr1:160577800-160583200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
19	chr1:160578000-160580200	Weak transcription	Primary B cells from cord blood	blood
20	chr1:160578000-160587400	Strong transcription	Primary B cells from peripheral blood	blood
21	chr1:160578200-160582800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr1:160578400-160581200	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr1:160579000-160584000	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr1:160579000-160589400	Strong transcription	GM12878-XiMat	blood
25	chr1:160579200-160580600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr1:160579200-160581200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr1:160579600-160583200	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr1:160579800-160583200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr1:160579800-160593200	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr1:160580000-160580800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr1:160580000-160581000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr1:160580000-160582800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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