Variant report

Variant	rs3765300
Chromosome Location	chr22:29628806-29628807
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr22:29626955-29629132	GM18951	blood:	n/a	n/a
2	POLR2A	chr22:29626413-29630403	GM12878	blood:	n/a	n/a
3	MAZ	chr22:29628691-29628831	HepG2	liver:	n/a	n/a
4	RCOR1	chr22:29628501-29628893	HepG2	liver:	n/a	n/a
5	POLR2A	chr22:29628319-29628945	GM12892	blood:	n/a	n/a
6	POLR2A	chr22:29625636-29630727	K562	blood:	n/a	n/a
7	POLR2A	chr22:29627501-29629586	GM12878	blood:	n/a	n/a
8	POLR2A	chr22:29627793-29629074	GM12878	blood:	n/a	n/a
9	POLR2A	chr22:29625696-29630751	PBDE	blood:	n/a	n/a
10	POLR2A	chr22:29628737-29628916	K562	blood:	n/a	n/a
11	POLR2A	chr22:29626882-29629668	GM19193	blood:	n/a	n/a
12	HEY1	chr22:29628472-29628837	HepG2	liver:	n/a	n/a
13	POLR2A	chr22:29626976-29628852	GM19099	blood:	n/a	n/a
14	ELF1	chr22:29628595-29628929	GM12878	blood:	n/a	n/a
15	MAX	chr22:29628282-29629058	HepG2	liver:	n/a	n/a
16	ELF1	chr22:29628582-29628856	HepG2	liver:	n/a	n/a

No data

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:29601210..29603979-chr22:29627327..29629637,2	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EWSR1-4	chr22:29627671-29629457	NONHSAT084681

No data

Variant related genes	Relation type
EMID1	TF binding region
ENSG00000186998	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12166644	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12628709	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16987313	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3765295	0.97[ASN][1000 genomes]
rs3765297	0.95[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs3950176	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5752884	0.91[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5752885	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5752887	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5752888	1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5752889	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5752895	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5763080	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5763084	0.97[ASN][1000 genomes]
rs5763087	0.91[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5763089	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5763091	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5763092	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5763093	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5763094	1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5763105	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5763110	0.90[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5763111	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6006068	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6006072	0.93[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6006073	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6006074	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6006075	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6006077	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	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	nsv524483	chr22:29525126-29630337	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	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
4	esv1806500	chr22:29604787-29635071	Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv522714	chr22:29612508-29630337	Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	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
7	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
rs3765300	TMEM211	cis	parietal	SCAN
rs3765300	PIWIL3	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29621800-29630200	Weak transcription	Brain Germinal Matrix	brain
2	chr22:29622000-29629000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr22:29622000-29655200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr22:29622000-29655800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr22:29622200-29629800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr22:29622400-29656600	Weak transcription	Colonic Mucosa	Colon
7	chr22:29622600-29641400	Weak transcription	Stomach Smooth Muscle	stomach
8	chr22:29626600-29630600	Enhancers	Spleen	Spleen
9	chr22:29627200-29629800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr22:29627600-29630200	Enhancers	Lung	lung
11	chr22:29627800-29629600	Enhancers	Liver	Liver
12	chr22:29627800-29629600	Enhancers	Gastric	stomach
13	chr22:29627800-29629800	Genic enhancers	Fetal Intestine Small	intestine
14	chr22:29627800-29630200	Enhancers	Ovary	ovary
15	chr22:29627800-29630200	Enhancers	Pancreas	Pancrea
16	chr22:29627800-29630600	Strong transcription	Dnd41	blood
17	chr22:29628200-29629000	Genic enhancers	Fetal Stomach	stomach
18	chr22:29628200-29629200	Flanking Active TSS	HepG2	liver
19	chr22:29628200-29629600	Enhancers	Adipose Nuclei	Adipose
20	chr22:29628200-29629600	Enhancers	Right Ventricle	heart
21	chr22:29628400-29629000	Enhancers	Fetal Muscle Leg	muscle
22	chr22:29628400-29629400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr22:29628400-29629400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr22:29628400-29629400	Enhancers	Right Atrium	heart
25	chr22:29628400-29629400	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr22:29628400-29629600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
27	chr22:29628400-29629600	Enhancers	Left Ventricle	heart
28	chr22:29628400-29629800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr22:29628400-29630200	Genic enhancers	Fetal Intestine Large	intestine
30	chr22:29628400-29641200	Weak transcription	Fetal Brain Male	brain
31	chr22:29628600-29629000	Enhancers	Brain Anterior Caudate	brain
32	chr22:29628600-29629800	Enhancers	HUVEC	blood vessel
33	chr22:29628600-29630600	Strong transcription	Fetal Brain Female	brain
34	chr22:29628800-29629000	Enhancers	Fetal Kidney	kidney
35	chr22:29628800-29630200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr22:29628800-29630400	Strong transcription	Fetal Lung	lung

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