Variant report

Variant	rs4820869
Chromosome Location	chr22:30986565-30986566
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr22:30986050-30988317	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr22:30985477-30988298	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:30983113..30985414-chr22:30986213..30988243,5	MCF-7	breast:
2	chr22:30968228..30973884-chr22:30985019..30988219,5	MCF-7	breast:
3	chr22:30984038..30987720-chr22:30992982..30995616,3	K562	blood:
4	chr22:30898269..30900043-chr22:30984977..30987505,2	K562	blood:
5	chr22:30969461..30973158-chr22:30985013..30988022,5	MCF-7	breast:
6	chr22:30970968..30972609-chr22:30985302..30987086,2	K562	blood:

No data

Variant related genes	Relation type
PES1	TF binding region
ENSG00000100029	Chromatin interaction
ENSG00000128242	Chromatin interaction
ENSG00000223831	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1008801	1.00[JPT][hapmap]
rs11912540	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11913206	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11913547	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11914005	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11914168	0.90[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12484495	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12484688	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13750	1.00[JPT][hapmap]
rs16988803	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.98[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16988810	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16988814	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17526668	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17670808	1.00[JPT][hapmap]
rs17738527	1.00[JPT][hapmap]
rs17738540	1.00[JPT][hapmap]
rs34236034	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820019	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820873	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820874	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820877	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6518693	1.00[JPT][hapmap]
rs7289820	1.00[JPT][hapmap]
rs73881484	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73881485	1.00[ASN][1000 genomes]
rs73881486	1.00[ASN][1000 genomes]
rs8138759	1.00[JPT][hapmap]
rs8141286	1.00[JPT][hapmap]
rs9606735	1.00[JPT][hapmap]
rs9606736	1.00[JPT][hapmap]
rs9606738	1.00[JPT][hapmap]
rs9606739	1.00[JPT][hapmap]
rs9608938	1.00[JPT][hapmap]
rs9608941	1.00[JPT][hapmap]
rs9608942	1.00[JPT][hapmap]
rs9608944	1.00[JPT][hapmap]
rs9608956	1.00[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	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv915818	chr22:30708245-31346302	Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv588887	chr22:30953521-30995356	Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv834175	chr22:30976624-31089545	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4820869	MTMR3	cis	cerebellum	SCAN
rs4820869	SLC35E4	cis	cerebellum	SCAN
rs4820869	C22orf27	cis	cerebellum	SCAN
rs4820869	TCN2	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30971000-30987200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr22:30972200-30986600	Weak transcription	Right Atrium	heart
3	chr22:30982800-30986600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr22:30983000-30986600	Weak transcription	Stomach Mucosa	stomach
5	chr22:30984600-30986600	Weak transcription	Fetal Kidney	kidney
6	chr22:30985000-30987000	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr22:30985400-30986600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr22:30985400-30986600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr22:30985400-30986600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr22:30985400-30986800	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr22:30985400-30986800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr22:30985400-30987000	Weak transcription	Placenta	Placenta
13	chr22:30985600-30986600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr22:30985600-30986600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr22:30985600-30986600	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr22:30985600-30986600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr22:30985600-30986600	Weak transcription	Esophagus	oesophagus
18	chr22:30985600-30986600	Weak transcription	Fetal Thymus	thymus
19	chr22:30985600-30986600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr22:30985600-30986600	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr22:30985600-30986800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr22:30985600-30986800	Enhancers	Brain Hippocampus Middle	brain
23	chr22:30985600-30986800	Weak transcription	Spleen	Spleen
24	chr22:30985600-30987000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr22:30985600-30987000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr22:30985600-30987000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr22:30985600-30987000	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr22:30985600-30987000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr22:30985600-30987200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr22:30985600-30987200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr22:30985600-30987200	Weak transcription	Aorta	Aorta
32	chr22:30985600-30987200	Weak transcription	Pancreas	Pancrea
33	chr22:30985800-30986600	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr22:30985800-30986600	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr22:30985800-30986600	Enhancers	Colon Smooth Muscle	Colon
36	chr22:30985800-30986600	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr22:30985800-30986600	Weak transcription	Fetal Intestine Large	intestine
38	chr22:30985800-30986600	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr22:30985800-30986600	Weak transcription	Thymus	Thymus
40	chr22:30985800-30986600	Enhancers	HepG2	liver
41	chr22:30985800-30987000	Weak transcription	Lung	lung
42	chr22:30986000-30986600	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr22:30986000-30986600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr22:30986000-30986600	Enhancers	Muscle Satellite Cultured Cells	--
45	chr22:30986000-30986600	Weak transcription	Fetal Brain Female	brain
46	chr22:30986000-30986600	Enhancers	HMEC	breast
47	chr22:30986000-30986600	Genic enhancers	NHEK	skin
48	chr22:30986000-30986800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr22:30986000-30986800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr22:30986000-30986800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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