Variant report

Variant	rs2289965
Chromosome Location	chr11:18728650-18728651
allele	C/T
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	PAX5	chr11:18728481-18728751	GM12878	blood:	n/a	n/a
2	POLR2A	chr11:18728381-18728661	GM12878	blood:	n/a	n/a
3	RCOR1	chr11:18728567-18728767	K562	blood:	n/a	n/a
4	MXI1	chr11:18726724-18728916	SK-N-SH	brain:	n/a	n/a
5	RXRA	chr11:18728424-18728784	GM12878	blood:	n/a	n/a
6	GATA2	chr11:18727987-18728931	SH-SY5Y	brain:	n/a	chr11:18728846-18728853 chr11:18728846-18728853 chr11:18728846-18728853
7	PAX5	chr11:18728282-18728812	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:18728261..18730822-chr11:18735824..18737369,2	K562	blood:
2	chr11:18721026..18722984-chr11:18728211..18731423,3	MCF-7	breast:

Variant related genes	Relation type
IGSF22	TF binding region
ENSG00000151117	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs10832986	1.00[LWK][hapmap]
rs12792924	1.00[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv553633	chr11:18311701-19058451	Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv1046886	chr11:18547568-18781448	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
3	nsv540956	chr11:18547568-18781448	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
4	nsv983163	chr11:18702181-18736146	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv897028	chr11:18714623-18770822	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv525192	chr11:18722791-18793360	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	esv3342768	chr11:18726926-18729124	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2289965	IGSF22	cis	lymphoblastoid	seeQTL
rs2289965	IGSF22	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18727000-18728800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
2	chr11:18727000-18728800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
3	chr11:18727000-18728800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr11:18727000-18728800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr11:18727000-18728800	Flanking Active TSS	Adipose Nuclei	Adipose
6	chr11:18727000-18729000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
7	chr11:18727000-18729000	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr11:18727200-18728800	Active TSS	Fetal Kidney	kidney
9	chr11:18727200-18730400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr11:18727400-18728800	Active TSS	Brain Anterior Caudate	brain
11	chr11:18727400-18729000	Active TSS	Colon Smooth Muscle	Colon
12	chr11:18727600-18728800	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr11:18727600-18728800	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr11:18727600-18728800	Active TSS	Brain Substantia Nigra	brain
15	chr11:18727600-18728800	Bivalent/Poised TSS	Osteobl	bone
16	chr11:18727800-18728800	Active TSS	Esophagus	oesophagus
17	chr11:18727800-18729000	Enhancers	Spleen	Spleen
18	chr11:18728000-18728800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr11:18728000-18728800	Flanking Active TSS	Duodenum Mucosa	Duodenum
20	chr11:18728000-18728800	Flanking Bivalent TSS/Enh	Placenta	Placenta
21	chr11:18728000-18728800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
22	chr11:18728000-18728800	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
23	chr11:18728200-18728800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr11:18728200-18728800	Flanking Active TSS	Brain Hippocampus Middle	brain
25	chr11:18728200-18728800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
26	chr11:18728200-18728800	Flanking Active TSS	Fetal Lung	lung
27	chr11:18728200-18728800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
28	chr11:18728200-18728800	Flanking Active TSS	Rectal Smooth Muscle	rectum
29	chr11:18728400-18728800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
30	chr11:18728400-18728800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr11:18728400-18728800	Flanking Active TSS	Brain Cingulate Gyrus	brain
32	chr11:18728400-18728800	Flanking Active TSS	Fetal Brain Female	brain
33	chr11:18728400-18728800	Flanking Active TSS	Fetal Intestine Small	intestine
34	chr11:18728400-18728800	Bivalent Enhancer	Fetal Thymus	thymus
35	chr11:18728400-18728800	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr11:18728400-18729000	Bivalent Enhancer	Fetal Muscle Leg	muscle
37	chr11:18728400-18729400	Enhancers	Lung	lung
38	chr11:18728400-18742200	Weak transcription	Gastric	stomach
39	chr11:18728600-18728800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr11:18728600-18728800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr11:18728600-18728800	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr11:18728600-18728800	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
43	chr11:18728600-18728800	Enhancers	Primary hematopoietic stem cells	blood
44	chr11:18728600-18728800	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr11:18728600-18728800	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr11:18728600-18728800	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
47	chr11:18728600-18728800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr11:18728600-18728800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr11:18728600-18728800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr11:18728600-18728800	Enhancers	Primary T killer memory cells from peripheral blood	blood

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