Variant report

Variant	rs11790744
Chromosome Location	chr9:6889793-6889794
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	SPI1	chr9:6889758-6890382	GM12878	blood:	n/a	chr9:6890083-6890096 chr9:6890080-6890089 chr9:6890084-6890093 chr9:6890059-6890072 chr9:6890061-6890070 chr9:6890082-6890095 chr9:6890060-6890073 chr9:6890083-6890096
2	SPI1	chr9:6889684-6890470	HL-60	blood:	n/a	chr9:6890387-6890400 chr9:6890083-6890096 chr9:6890080-6890089 chr9:6890084-6890093 chr9:6890059-6890072 chr9:6890061-6890070 chr9:6890082-6890095 chr9:6890060-6890073 chr9:6890083-6890096

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:6888137..6890891-chr9:6891909..6894488,2	K562	blood:

Variant related genes	Relation type
KDM4C	TF binding region
ENSG00000107077	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10815474	0.92[JPT][hapmap];0.82[YRI][hapmap]
rs10975861	0.93[CEU][hapmap];0.87[CHD][hapmap];0.88[TSI][hapmap];0.80[EUR][1000 genomes]
rs10975871	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs10975875	0.97[ASN][1000 genomes]
rs10975883	0.92[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11788152	0.86[ASN][1000 genomes]
rs11788187	0.86[ASN][1000 genomes]
rs11788687	0.86[ASN][1000 genomes]
rs11788849	0.85[ASN][1000 genomes]
rs11789124	0.85[ASN][1000 genomes]
rs11789248	0.85[ASN][1000 genomes]
rs11789250	0.85[ASN][1000 genomes]
rs11792447	0.92[CHB][hapmap];0.85[ASN][1000 genomes]
rs11794598	0.85[ASN][1000 genomes]
rs11794707	0.85[CHB][hapmap];1.00[CHD][hapmap];0.85[ASN][1000 genomes]
rs11794732	0.85[ASN][1000 genomes]
rs12375929	0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12686353	0.83[CHD][hapmap]
rs17511187	0.85[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs17511250	0.85[CHB][hapmap];1.00[CHD][hapmap]
rs17595667	0.85[CHB][hapmap];1.00[CHD][hapmap];0.85[ASN][1000 genomes]
rs17595843	0.86[ASN][1000 genomes]
rs17595877	0.85[CHB][hapmap];1.00[CHD][hapmap];0.86[ASN][1000 genomes]
rs17595898	0.86[ASN][1000 genomes]
rs17596052	0.83[CHD][hapmap]
rs35732562	1.00[ASW][hapmap];0.93[CEU][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.86[MKK][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3818891	0.81[CHD][hapmap]
rs55686117	0.86[ASN][1000 genomes]
rs55790433	0.86[ASN][1000 genomes]
rs56036039	0.86[ASN][1000 genomes]
rs56185621	0.85[ASN][1000 genomes]
rs56225816	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56279813	0.86[ASN][1000 genomes]
rs56357252	0.86[ASN][1000 genomes]
rs57005961	0.87[ASN][1000 genomes]
rs57463825	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58143962	0.85[ASN][1000 genomes]
rs58213169	0.86[ASN][1000 genomes]
rs58307562	0.85[ASN][1000 genomes]
rs58361204	0.86[ASN][1000 genomes]
rs58378352	0.86[ASN][1000 genomes]
rs58977474	0.86[ASN][1000 genomes]
rs59636651	0.85[ASN][1000 genomes]
rs59779500	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59999598	0.86[ASN][1000 genomes]
rs60173310	0.84[ASN][1000 genomes]
rs61204407	0.84[ASN][1000 genomes]
rs62533762	0.85[ASN][1000 genomes]
rs62533769	0.86[ASN][1000 genomes]
rs62533773	0.86[ASN][1000 genomes]
rs62533774	0.86[ASN][1000 genomes]
rs62533787	0.86[ASN][1000 genomes]
rs62533788	0.86[ASN][1000 genomes]
rs62533789	0.86[ASN][1000 genomes]
rs62533791	0.86[ASN][1000 genomes]
rs62533792	0.86[ASN][1000 genomes]
rs62533794	0.85[ASN][1000 genomes]
rs62533818	0.84[ASN][1000 genomes]
rs62533819	0.85[ASN][1000 genomes]
rs62533820	0.86[ASN][1000 genomes]
rs62533821	0.86[ASN][1000 genomes]
rs62533822	0.86[ASN][1000 genomes]
rs62533823	0.86[ASN][1000 genomes]
rs62533824	0.85[ASN][1000 genomes]
rs62533825	0.87[ASN][1000 genomes]
rs62533827	0.87[ASN][1000 genomes]
rs62533828	0.87[ASN][1000 genomes]
rs62533829	0.87[ASN][1000 genomes]
rs62533830	0.87[ASN][1000 genomes]
rs62533831	0.87[ASN][1000 genomes]
rs62533832	0.87[ASN][1000 genomes]
rs62533833	0.87[ASN][1000 genomes]
rs62533834	0.87[ASN][1000 genomes]
rs67642242	0.87[ASN][1000 genomes]
rs67866005	0.87[ASN][1000 genomes]
rs68190370	0.86[ASN][1000 genomes]
rs7033444	0.92[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs72701484	0.86[ASN][1000 genomes]
rs72701487	0.83[ASN][1000 genomes]
rs73405231	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73410616	0.86[ASN][1000 genomes]
rs73639387	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7867935	0.93[CEU][hapmap]
rs946926	0.92[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752308	chr9:6523060-6899149	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv870402	chr9:6565246-7016784	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
3	nsv1033539	chr9:6566610-7022554	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
4	nsv466111	chr9:6567841-7017391	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
5	nsv613208	chr9:6567841-7017391	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
6	nsv1024831	chr9:6573752-7018641	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	70 gene(s)	inside rSNPs	diseases
7	nsv892166	chr9:6602821-7222495	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
8	esv2752309	chr9:6670448-6908200	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	70 gene(s)	inside rSNPs	diseases
9	nsv892181	chr9:6680477-7070962	Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	70 gene(s)	inside rSNPs	diseases
10	nsv870332	chr9:6694842-6911550	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
11	nsv1016109	chr9:6712314-6924843	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
12	nsv613252	chr9:6715730-7022554	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
13	nsv831499	chr9:6723287-6930933	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
14	nsv1018557	chr9:6723728-6891136	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
15	nsv1023906	chr9:6731786-7372132	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
16	nsv1023461	chr9:6774993-7022554	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv831500	chr9:6847952-6992535	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	esv1801159	chr9:6865386-6901008	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
19	nsv831501	chr9:6868099-7058526	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
20	esv2426665	chr9:6888178-6889824	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11790744	GLDC	cis	cerebellum	SCAN
rs11790744	KDM4C	cis	cerebellum	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6824400-6892000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr9:6835400-6893200	Weak transcription	Colonic Mucosa	Colon
3	chr9:6869200-6898000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr9:6869600-6909400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr9:6869800-6890000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr9:6869800-6908000	Weak transcription	Fetal Stomach	stomach
7	chr9:6871000-6902200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr9:6871200-6889800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr9:6871200-6896000	Weak transcription	NHEK	skin
10	chr9:6873600-6896800	Weak transcription	Stomach Mucosa	stomach
11	chr9:6874200-6893200	Weak transcription	Brain Anterior Caudate	brain
12	chr9:6874200-6902400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr9:6874400-6893200	Weak transcription	Brain Hippocampus Middle	brain
14	chr9:6874400-6896600	Weak transcription	Brain Substantia Nigra	brain
15	chr9:6875000-6902600	Weak transcription	HSMM	muscle
16	chr9:6875800-6893400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr9:6876600-6893200	Weak transcription	Thymus	Thymus
18	chr9:6876800-6893400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr9:6877800-6896600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr9:6878200-6902400	Weak transcription	NHDF-Ad	bronchial
21	chr9:6878600-6896600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr9:6878600-6897800	Weak transcription	HSMMtube	muscle
23	chr9:6878800-6893600	Weak transcription	HMEC	breast
24	chr9:6879000-6896600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr9:6879800-6902400	Weak transcription	Osteobl	bone
26	chr9:6880600-6889800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr9:6880800-6893000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr9:6880800-6907000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr9:6881200-6892800	Weak transcription	Dnd41	blood
30	chr9:6882800-6912000	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr9:6883000-6911800	Weak transcription	Psoas Muscle	Psoas
32	chr9:6884000-6897400	Weak transcription	Fetal Kidney	kidney
33	chr9:6884400-6896000	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr9:6884400-6896600	Weak transcription	Fetal Lung	lung
35	chr9:6884800-6893200	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr9:6885400-6892600	Weak transcription	K562	blood
37	chr9:6885600-6893200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr9:6886000-6896800	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr9:6886200-6892600	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr9:6886600-6890400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr9:6887000-6890200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr9:6887000-6890800	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr9:6887000-6891200	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr9:6887000-6891200	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr9:6887000-6891200	Strong transcription	Fetal Thymus	thymus
46	chr9:6887200-6896800	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr9:6887400-6893200	Weak transcription	Brain Cingulate Gyrus	brain
48	chr9:6887600-6891000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr9:6887600-6892400	Weak transcription	Hela-S3	cervix
50	chr9:6887600-6896800	Weak transcription	Fetal Brain Male	brain

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