Variant report

Variant	rs11971770
Chromosome Location	chr7:150259751-150259752
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	GATA2	chr7:150259735-150260740	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr7:150259671-150260870	HUVEC	blood vessel:	n/a	n/a

Variant related genes	Relation type
GIMAP4	TF binding region

Extended variants
information (count: 54 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10085891	0.82[EUR][1000 genomes]
rs10216102	0.90[EUR][1000 genomes]
rs10224387	0.81[CEU][hapmap];0.83[TSI][hapmap]
rs10227094	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10239578	0.89[EUR][1000 genomes]
rs10240209	0.90[EUR][1000 genomes]
rs10248553	0.80[EUR][1000 genomes]
rs10255487	0.89[EUR][1000 genomes]
rs10270122	0.90[EUR][1000 genomes]
rs10273606	0.95[CEU][hapmap];0.86[CHB][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11975418	0.87[EUR][1000 genomes]
rs11984138	0.88[EUR][1000 genomes]
rs12671922	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1317276	0.95[CEU][hapmap];0.91[CHB][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1533847	0.86[CHB][hapmap]
rs1916027	0.90[EUR][1000 genomes]
rs2140138	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140139	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28409283	0.97[ASN][1000 genomes]
rs28537284	0.92[EUR][1000 genomes]
rs28829297	0.90[EUR][1000 genomes]
rs4143732	0.90[EUR][1000 genomes]
rs55653011	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56158089	0.92[EUR][1000 genomes]
rs57604196	0.86[EUR][1000 genomes]
rs60628216	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6464081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6959171	0.95[CEU][hapmap];0.86[CHB][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6959264	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6961075	0.93[EUR][1000 genomes]
rs73727323	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73727325	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73727338	0.89[EUR][1000 genomes]
rs7781704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7782221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7787987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7797456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7800143	0.83[EUR][1000 genomes]
rs7800829	0.86[JPT][hapmap]
rs7802869	0.95[EUR][1000 genomes]
rs7806724	0.95[CEU][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs952642	0.95[EUR][1000 genomes]
rs9640279	0.95[CEU][hapmap];0.86[CHB][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv1015582	chr7:149967986-150285104	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv1025129	chr7:150146593-150266217	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	esv3395746	chr7:150181141-150300680	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
8	esv3341786	chr7:150220353-150269134	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	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
10	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
11	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11971770	TMEM176B	cis	cerebellum	SCAN
rs11971770	ATP6V0E2	cis	parietal	SCAN
rs11971770	HCA112	cis	multi-tissue	Pritchard
rs11971770	GIMAP4	cis	parietal	SCAN
rs11971770	LR8	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150257600-150260400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
2	chr7:150258000-150260400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr7:150258600-150261000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr7:150258800-150260000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
5	chr7:150258800-150260000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
6	chr7:150258800-150261600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
7	chr7:150259000-150260000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr7:150259000-150262600	Enhancers	HUVEC	blood vessel
9	chr7:150259200-150260400	Enhancers	Primary T cells fromperipheralblood	blood
10	chr7:150259200-150260400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr7:150259400-150259800	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr7:150259400-150259800	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr7:150259400-150260800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood

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