Variant report

Variant	rs11984138
Chromosome Location	chr7:150300735-150300736
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GIMAP6-1	chr7:150300649-150301732	NONHSAT124145

Extended variants
information (count: 69 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10085891	0.83[EUR][1000 genomes]
rs10216102	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10224387	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10227094	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10232947	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10235151	0.81[ASW][hapmap];0.82[CEU][hapmap];0.84[LWK][hapmap];0.82[MKK][hapmap];0.88[YRI][hapmap]
rs10239578	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10240209	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10248553	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10255487	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10270122	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10273606	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11971770	0.95[CEU][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs11975418	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12671922	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1317276	0.93[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1916027	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2140138	0.95[CEU][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs2140139	0.88[EUR][1000 genomes]
rs2140145	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28537284	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28829297	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3088115	0.81[ASW][hapmap];0.82[CEU][hapmap];0.82[CHB][hapmap]
rs3735085	0.87[ASW][hapmap];0.82[CEU][hapmap];0.82[CHB][hapmap];0.92[LWK][hapmap];0.91[MKK][hapmap];0.92[YRI][hapmap]
rs4143732	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55653011	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56158089	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57604196	0.84[EUR][1000 genomes]
rs60628216	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6464081	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs6959171	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6959264	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6961075	0.95[EUR][1000 genomes]
rs73727323	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73727325	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73727338	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7781704	0.86[EUR][1000 genomes]
rs7782221	0.88[EUR][1000 genomes]
rs7787987	0.88[EUR][1000 genomes]
rs7797456	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs7800143	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7802869	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7806724	0.87[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs952642	0.93[EUR][1000 genomes]
rs9640279	0.87[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034409	chr7:149844639-150447071	Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv608990	chr7:149961274-150707488	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv1017368	chr7:150016952-150655773	Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv539195	chr7:150016952-150655773	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	esv16529	chr7:150249312-150312843	Genic enhancers Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	esv2758617	chr7:150251949-150463804	Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	esv2759573	chr7:150251949-150463804	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	esv1793193	chr7:150285801-150301569	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases
9	esv1800872	chr7:150285801-150301569	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases
10	esv1804946	chr7:150285801-150301569	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	lncRNA	n/a	inside rSNPs	diseases
11	esv1814847	chr7:150285801-150301569	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases
12	esv1835596	chr7:150285801-150301569	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases
13	esv1841982	chr7:150285801-150301569	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	lncRNA	n/a	inside rSNPs	diseases
14	nsv442238	chr7:150285801-150301569	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases
15	esv13954	chr7:150292485-150307048	Enhancers Weak transcription Flanking Active TSS	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
16	esv3490967	chr7:150293370-150301941	Enhancers Weak transcription Flanking Active TSS	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
17	esv3490968	chr7:150293370-150301941	Enhancers Weak transcription Flanking Active TSS	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
18	nsv511998	chr7:150299281-150306979	Enhancers Weak transcription Flanking Active TSS	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
19	esv3366219	chr7:150299819-150305317	Flanking Active TSS Weak transcription Enhancers	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
20	esv1005919	chr7:150299834-150306808	Weak transcription Enhancers Flanking Active TSS	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
21	esv3431995	chr7:150299969-150305067	Weak transcription Flanking Active TSS Enhancers	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
22	esv3478424	chr7:150299997-150302657	Enhancers Weak transcription Flanking Active TSS	lncRNA	n/a	inside rSNPs	diseases
23	esv3478425	chr7:150299997-150302657	Enhancers Weak transcription Flanking Active TSS	lncRNA	n/a	inside rSNPs	diseases
24	esv3323446	chr7:150300519-150305817	Enhancers Weak transcription Flanking Active TSS	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11984138	LR8	cis	multi-tissue	Pritchard
rs11984138	HCA112	cis	multi-tissue	Pritchard
rs11984138	COL8A2	trans	parietal	SCAN
rs11984138	ATP6V0E2	cis	parietal	SCAN
rs11984138	GIMAP4	cis	parietal	SCAN
rs11984138	GIMAP5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150300200-150300800	Enhancers	Primary T killer memory cells from peripheral blood	blood
2	chr7:150300200-150301000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
3	chr7:150300200-150301200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr7:150300200-150301400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr7:150300200-150301600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr7:150300200-150301800	Enhancers	Primary T cells from cord blood	blood
7	chr7:150300200-150301800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr7:150300200-150303000	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr7:150300400-150301400	Enhancers	Dnd41	blood
10	chr7:150300600-150301400	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr7:150300600-150301800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr7:150300600-150302200	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr7:150300600-150316800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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