Variant report

Variant	rs2301290
Chromosome Location	chr22:29661341-29661342
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	chr22:29660900-29661580	HepG2	liver:	n/a	n/a
2	POLR2A	chr22:29661211-29662046	GM12891	blood:	n/a	n/a
3	POLR2A	chr22:29661169-29667225	GM12878	blood:	n/a	n/a
4	POLR2A	chr22:29661210-29661385	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr22:29661184-29664672	GM12878	blood:	n/a	n/a
6	POLR2A	chr22:29661114-29667320	SK-N-MC	brain:	n/a	n/a
7	POLR2A	chr22:29661270-29661395	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:29660929..29666447-chr22:29700529..29705135,9	K562	blood:
2	chr22:29654217..29657445-chr22:29658284..29661902,3	MCF-7	breast:

Variant related genes	Relation type
EWSR1	TF binding region
RHBDD3	TF binding region
ENSG00000237015	Chromatin interaction
ENSG00000185340	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11090564	0.94[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs131180	0.88[ASN][1000 genomes]
rs131182	0.83[ASN][1000 genomes]
rs131189	0.82[ASN][1000 genomes]
rs140062	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.88[ASN][1000 genomes]
rs140063	0.88[ASN][1000 genomes]
rs140066	0.81[ASN][1000 genomes]
rs16987328	1.00[ASW][hapmap]
rs174759	0.84[ASN][1000 genomes]
rs174761	1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs174762	1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[JPT][hapmap]
rs174764	1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap]
rs174766	1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap]
rs174770	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs2071578	1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap]
rs2072051	0.88[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap]
rs2267132	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs2267133	0.88[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap]
rs2283849	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs2283850	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs2301585	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs2857466	0.84[CHD][hapmap];0.83[JPT][hapmap]
rs28755	0.82[ASN][1000 genomes]
rs3788410	1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs3788411	1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap]
rs4820803	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4820804	1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs5752903	0.88[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap]
rs5763138	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs5763139	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs6006090	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs6006098	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs715494	0.88[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap]
rs762817	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs879580	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9537	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs98069	1.00[CHB][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	esv1809952	chr22:29595349-29661434	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv829154	chr22:29617485-29724001	Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv834171	chr22:29626402-29829844	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2301290	SEZ6L	cis	cerebellum	SCAN
rs2301290	ENSG00000100263	cis	multi-tissue	Pritchard

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29641600-29661800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr22:29642600-29662400	Strong transcription	Fetal Intestine Small	intestine
3	chr22:29647400-29662000	Strong transcription	Fetal Stomach	stomach
4	chr22:29649000-29662400	Weak transcription	Fetal Brain Male	brain
5	chr22:29650200-29662600	Weak transcription	Stomach Mucosa	stomach
6	chr22:29653600-29662200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr22:29654200-29662600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr22:29654600-29662200	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr22:29654600-29662400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr22:29654600-29662400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr22:29654600-29662600	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr22:29654800-29662400	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr22:29655600-29662800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr22:29658200-29662200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr22:29658200-29662200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr22:29658200-29662400	Weak transcription	Right Atrium	heart
17	chr22:29658400-29662800	Weak transcription	Primary B cells from cord blood	blood
18	chr22:29658600-29662600	Weak transcription	Psoas Muscle	Psoas
19	chr22:29658800-29661400	Strong transcription	Fetal Muscle Trunk	muscle
20	chr22:29659200-29662000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr22:29659400-29661400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr22:29659400-29661400	Strong transcription	Brain Anterior Caudate	brain
23	chr22:29659400-29662000	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr22:29659400-29662000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr22:29659400-29662000	Weak transcription	Hela-S3	cervix
26	chr22:29659600-29661400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr22:29659600-29661400	Strong transcription	Fetal Lung	lung
28	chr22:29659600-29661400	Strong transcription	Dnd41	blood
29	chr22:29659600-29661600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr22:29659600-29661600	Strong transcription	Liver	Liver
31	chr22:29659600-29661600	Strong transcription	Brain Cingulate Gyrus	brain
32	chr22:29659600-29661600	Strong transcription	Colon Smooth Muscle	Colon
33	chr22:29659600-29661800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr22:29659600-29661800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr22:29659600-29661800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr22:29659600-29661800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr22:29659600-29661800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr22:29659600-29661800	Strong transcription	Brain Germinal Matrix	brain
39	chr22:29659600-29661800	Strong transcription	Brain Hippocampus Middle	brain
40	chr22:29659600-29661800	Strong transcription	Fetal Intestine Large	intestine
41	chr22:29659600-29661800	Strong transcription	Lung	lung
42	chr22:29659600-29661800	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr22:29659600-29661800	Strong transcription	Right Ventricle	heart
44	chr22:29659600-29661800	Strong transcription	Stomach Smooth Muscle	stomach
45	chr22:29659600-29661800	Strong transcription	Thymus	Thymus
46	chr22:29659600-29662000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr22:29659600-29662000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr22:29659600-29662000	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr22:29659600-29662000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr22:29659600-29662000	Strong transcription	Adipose Nuclei	Adipose

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