Variant report

Variant	rs9657891
Chromosome Location	chr7:150435473-150435474
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	POLR2A	chr7:150434287-150436204	GM12891	blood:	n/a	n/a
2	POLR2A	chr7:150434050-150436345	GM12892	blood:	n/a	n/a
3	POLR2A	chr7:150434332-150436034	GM12892	blood:	n/a	n/a
4	POLR2A	chr7:150434081-150436563	GM12892	blood:	n/a	n/a
5	POLR2A	chr7:150433739-150436135	GM12891	blood:	n/a	n/a
6	POLR2A	chr7:150434323-150435508	GM12891	blood:	n/a	n/a
7	POLR2A	chr7:150434201-150436185	GM12892	blood:	n/a	n/a
8	POLR2A	chr7:150433977-150436489	GM12892	blood:	n/a	n/a
9	POLR2A	chr7:150434082-150436015	GM18505	blood:	n/a	n/a
10	MTA3	chr7:150433963-150436163	GM12878	blood:	n/a	n/a
11	POLR2A	chr7:150434252-150435970	GM12891	blood:	n/a	n/a
12	POLR2A	chr7:150435320-150435956	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:150433868..150435484-chr7:150436619..150439022,2	MCF-7	breast:

Variant related genes	Relation type
GIMAP5	TF binding region
ENSG00000196329	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10237852	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1860870	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2058447	0.96[CEU][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2373851	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3757411	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.84[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6464096	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6972271	0.96[CEU][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6979154	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
6	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
7	nsv1030109	chr7:150312916-150701010	Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
8	nsv967475	chr7:150323577-150610034	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv831187	chr7:150325913-150503500	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs9657891	GIMAP8	cis	parietal	SCAN
rs9657891	GIMAP5	cis	normal skin	skin_eQTL
rs9657891	GIMAP5	cis	lymphoblastoid	seeQTL
rs9657891	LR8	cis	multi-tissue	Pritchard
rs9657891	IAN4L1	cis	multi-tissue	Pritchard
rs9657891	GIMAP6	Cis_1M	lymphoblastoid	RTeQTL
rs9657891	ABP1	cis	multi-tissue	Pritchard
rs9657891	GIMAP5	cis	multi-tissue	Pritchard
rs9657891	HCA112	cis	multi-tissue	Pritchard

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150433800-150436800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
2	chr7:150433800-150439200	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr7:150434000-150435800	Active TSS	Gastric	stomach
4	chr7:150434000-150435800	Active TSS	Spleen	Spleen
5	chr7:150434000-150436200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr7:150434000-150436800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr7:150434000-150436800	Active TSS	Sigmoid Colon	Sigmoid Colon
8	chr7:150434000-150437000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr7:150434000-150437200	Active TSS	Primary T helper naive cells from peripheral blood	blood
10	chr7:150434000-150437400	Active TSS	Brain Anterior Caudate	brain
11	chr7:150434000-150437400	Active TSS	Colonic Mucosa	Colon
12	chr7:150434000-150437600	Active TSS	Lung	lung
13	chr7:150434000-150437600	Active TSS	Rectal Mucosa Donor 31	rectum
14	chr7:150434000-150437600	Active TSS	Right Ventricle	heart
15	chr7:150434000-150437800	Active TSS	Rectal Smooth Muscle	rectum
16	chr7:150434000-150438000	Active TSS	Right Atrium	heart
17	chr7:150434200-150435800	Active TSS	Primary T killer memory cells from peripheral blood	blood
18	chr7:150434200-150435800	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
19	chr7:150434200-150435800	Bivalent/Poised TSS	Placenta	Placenta
20	chr7:150434200-150435800	Active TSS	Pancreas	Pancrea
21	chr7:150434200-150436000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
22	chr7:150434200-150436000	Active TSS	Esophagus	oesophagus
23	chr7:150434200-150436200	Flanking Active TSS	Primary hematopoietic stem cells	blood
24	chr7:150434200-150437000	Active TSS	Primary T cells from cord blood	blood
25	chr7:150434200-150437200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
26	chr7:150434200-150437200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
27	chr7:150434200-150437400	Active TSS	Primary T cells fromperipheralblood	blood
28	chr7:150434200-150437600	Active TSS	Brain Hippocampus Middle	brain
29	chr7:150434200-150437600	Active TSS	Left Ventricle	heart
30	chr7:150434200-150437600	Active TSS	Skeletal Muscle Female	skeletal muscle
31	chr7:150434200-150437800	Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr7:150434200-150437800	Active TSS	Skeletal Muscle Male	skeletal muscle
33	chr7:150434200-150438000	Active TSS	Duodenum Mucosa	Duodenum
34	chr7:150434200-150438000	Active TSS	Psoas Muscle	Psoas
35	chr7:150434400-150435600	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
36	chr7:150434400-150435600	Active TSS	Ovary	ovary
37	chr7:150434400-150435800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
38	chr7:150434400-150435800	Active TSS	Colon Smooth Muscle	Colon
39	chr7:150434400-150436000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
40	chr7:150434400-150436000	Active TSS	Fetal Kidney	kidney
41	chr7:150434400-150436000	Flanking Active TSS	Fetal Thymus	thymus
42	chr7:150434400-150436200	Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr7:150434400-150436400	Flanking Active TSS	HUVEC	blood vessel
44	chr7:150434400-150436600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
45	chr7:150434400-150436800	Active TSS	Brain Substantia Nigra	brain
46	chr7:150434400-150437200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr7:150434400-150437200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
48	chr7:150434400-150437400	Active TSS	Brain Angular Gyrus	brain
49	chr7:150434400-150437400	Active TSS	Thymus	Thymus
50	chr7:150434400-150437800	Active TSS	Adipose Nuclei	Adipose

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