Variant report

Variant	rs2299830
Chromosome Location	chr22:30817631-30817632
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:73)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:73 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr22:30817434-30821076	HUVEC	blood vessel:	n/a	n/a
2	GATA1	chr22:30816326-30818234	PBDE	blood:	n/a	n/a
3	CEBPD	chr22:30817519-30818106	K562	blood:	n/a	n/a
4	CEBPB	chr22:30817372-30817985	K562	blood:	n/a	n/a
5	POLR2A	chr22:30817531-30818614	K562	blood:	n/a	n/a
6	KAP1	chr22:30817398-30818238	U2OS	brain:	n/a	n/a
7	TEAD4	chr22:30817379-30818092	HepG2	liver:	n/a	n/a
8	POLR2A	chr22:30816349-30821249	IMR90	lung:	n/a	n/a
9	FOS	chr22:30817505-30817951	HUVEC	blood vessel:	n/a	n/a
10	PML	chr22:30817525-30818095	K562	blood:	n/a	n/a
11	TBP	chr22:30817577-30818176	HepG2	liver:	n/a	n/a
12	TAF1	chr22:30817520-30817866	K562	blood:	n/a	n/a
13	HEY1	chr22:30817573-30817893	K562	blood:	n/a	n/a
14	POLR2A	chr22:30817509-30822980	HUVEC	blood vessel:	n/a	n/a
15	CHD1	chr22:30816159-30822993	IMR90	lung:	n/a	n/a
16	GATA2	chr22:30817583-30818126	HUVEC	blood vessel:	n/a	chr22:30817780-30817794 chr22:30817839-30817853
17	MAFF	chr22:30817388-30818319	K562	blood:	n/a	n/a
18	HNF4G	chr22:30817588-30818367	HepG2	liver:	n/a	chr22:30817937-30817945 chr22:30817938-30817946
19	POLR2A	chr22:30816245-30822974	PBDE	blood:	n/a	n/a
20	POLR2A	chr22:30817129-30818359	HUVEC	blood vessel:	n/a	n/a
21	NR2F2	chr22:30817496-30818454	K562	blood:	n/a	n/a
22	CCNT2	chr22:30817620-30817998	K562	blood:	n/a	n/a
23	TBL1XR1	chr22:30817631-30818391	K562	blood:	n/a	n/a
24	POLR2A	chr22:30817578-30818333	HepG2	liver:	n/a	n/a
25	FOXA2	chr22:30817628-30818170	HepG2	liver:	n/a	n/a
26	TRIM28	chr22:30817572-30818363	K562	blood:	n/a	n/a
27	CBX3	chr22:30817524-30818069	K562	blood:	n/a	n/a
28	GATA2	chr22:30817531-30818047	K562	blood:	n/a	chr22:30817780-30817794 chr22:30817839-30817853
29	EP300	chr22:30817631-30818058	K562	blood:	n/a	n/a
30	POLR2A	chr22:30817570-30818193	HUVEC	blood vessel:	n/a	n/a
31	MYC	chr22:30817561-30818259	K562	blood:	n/a	n/a
32	GATA1	chr22:30817579-30818310	K562	blood:	n/a	n/a
33	POLR2A	chr22:30817536-30820541	HepG2	liver:	n/a	n/a
34	RCOR1	chr22:30816050-30822994	IMR90	lung:	n/a	n/a
35	EP300	chr22:30817613-30818075	GM12878	blood:	n/a	n/a
36	KAP1	chr22:30817581-30818383	HEK293	kidney:	n/a	n/a
37	POLR2A	chr22:30817549-30818323	K562	blood:	n/a	n/a
38	EP300	chr22:30817573-30818129	HepG2	liver:	n/a	n/a
39	HEY1	chr22:30817578-30818389	HepG2	liver:	n/a	n/a
40	ARID3A	chr22:30817570-30818253	K562	blood:	n/a	n/a
41	CEBPB	chr22:30817568-30818017	K562	blood:	n/a	n/a
42	TEAD4	chr22:30817467-30818443	K562	blood:	n/a	n/a
43	POLR2A	chr22:30817579-30820313	K562	blood:	n/a	n/a
44	POLR2A	chr22:30817583-30818379	K562	blood:	n/a	n/a
45	TEAD4	chr22:30817526-30818022	K562	blood:	n/a	n/a
46	TAL1	chr22:30817568-30818348	K562	blood:	n/a	n/a
47	POLR2A	chr22:30817614-30817989	U87	brain:	n/a	n/a
48	BHLHE40	chr22:30817398-30818070	K562	blood:	n/a	n/a
49	JUND	chr22:30817579-30818320	K562	blood:	n/a	n/a
50	MXI1	chr22:30817464-30820543	IMR90	lung:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:30814763..30819112-chr22:30819393..30823307,5	MCF-7	breast:
2	chr22:30816361..30822733-chr22:30829064..30833429,8	K562	blood:
3	chr22:30812731..30815358-chr22:30815799..30818479,2	MCF-7	breast:
4	chr22:30793027..30795107-chr22:30817004..30819701,2	K562	blood:
5	chr22:30641395..30644994-chr22:30815782..30819866,5	MCF-7	breast:
6	chr22:30791754..30798377-chr22:30814746..30822334,13	K562	blood:
7	chr22:30801331..30806439-chr22:30816907..30821751,5	K562	blood:
8	chr22:30780386..30782265-chr22:30815840..30818586,2	MCF-7	breast:
9	chr22:30787731..30797808-chr22:30813672..30825727,31	MCF-7	breast:

No data

Variant related genes	Relation type
MTFP1	TF binding region
ENSG00000268538	TF binding region
ENSG00000272689	TF binding region
ENSG00000203606	Chromatin interaction
ENSG00000268538	Chromatin interaction
ENSG00000242114	Chromatin interaction
ENSG00000268812	Chromatin interaction
ENSG00000100003	Chromatin interaction
ENSG00000128342	Chromatin interaction
ENSG00000099999	Chromatin interaction
ENSG00000249590	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1009337	0.85[MEX][hapmap]
rs10376	0.82[CHB][hapmap];0.85[CHD][hapmap];0.88[ASN][1000 genomes]
rs10427610	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1043099	0.88[ASN][1000 genomes]
rs1046199	0.92[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2108093	0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4339043	0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4820008	0.88[ASN][1000 genomes]
rs4820831	0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs4820844	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4820846	0.88[EUR][1000 genomes]
rs4820847	0.88[EUR][1000 genomes]
rs4823085	0.86[ASN][1000 genomes]
rs5749066	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs5749078	0.88[ASN][1000 genomes]
rs5749082	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5753071	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs5753080	0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs5753088	0.81[ASN][1000 genomes]
rs5753111	0.88[ASN][1000 genomes]
rs5753124	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs5763923	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs5997642	0.84[CEU][hapmap];0.82[CHB][hapmap];0.88[EUR][1000 genomes]
rs7284527	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs737723	0.88[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs737950	0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs740219	0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs929454	0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9608904	1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9619104	0.88[ASN][1000 genomes]
rs9620979	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv914970	chr22:30619599-30850395	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2299830	OR4N5	trans	cerebellum	SCAN
rs2299830	RFPL2	cis	parietal	SCAN
rs2299830	SF3A1	cis	multi-tissue	Pritchard
rs2299830	PAIP2B	trans	cerebellum	SCAN
rs2299830	ZNF284	trans	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30794000-30818000	Weak transcription	Right Atrium	heart
2	chr22:30794800-30818600	Weak transcription	Primary B cells from cord blood	blood
3	chr22:30805000-30818200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr22:30809000-30818200	Strong transcription	Fetal Brain Female	brain
5	chr22:30809800-30818400	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr22:30809800-30818400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr22:30810000-30817800	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr22:30810600-30817800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr22:30811000-30818000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr22:30811800-30818200	Strong transcription	Primary T cells from cord blood	blood
11	chr22:30812400-30818200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr22:30812600-30817800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr22:30812600-30818800	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr22:30812800-30818000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr22:30812800-30818200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr22:30812800-30818400	Weak transcription	Fetal Brain Male	brain
17	chr22:30813000-30817800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr22:30813400-30818400	Genic enhancers	HMEC	breast
19	chr22:30813800-30817800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr22:30813800-30817800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr22:30814000-30818800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr22:30814600-30817800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr22:30814600-30818600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr22:30814600-30818600	Enhancers	Fetal Intestine Large	intestine
25	chr22:30814800-30817800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr22:30814800-30818200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr22:30814800-30819000	Weak transcription	Aorta	Aorta
28	chr22:30815000-30817800	Weak transcription	Left Ventricle	heart
29	chr22:30815000-30818400	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr22:30815200-30817800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr22:30815200-30818000	Weak transcription	Colon Smooth Muscle	Colon
32	chr22:30815200-30818000	Weak transcription	Esophagus	oesophagus
33	chr22:30815200-30818000	Weak transcription	Fetal Lung	lung
34	chr22:30815200-30818200	Weak transcription	Adipose Nuclei	Adipose
35	chr22:30815200-30818400	Weak transcription	Thymus	Thymus
36	chr22:30815200-30818600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr22:30815200-30818600	Weak transcription	Fetal Kidney	kidney
38	chr22:30815200-30818600	Genic enhancers	NHEK	skin
39	chr22:30815400-30818000	Weak transcription	Pancreas	Pancrea
40	chr22:30815400-30818200	Weak transcription	Spleen	Spleen
41	chr22:30815600-30818000	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr22:30815800-30818400	Genic enhancers	HSMM	muscle
43	chr22:30816200-30817800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr22:30816200-30817800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr22:30816200-30818000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr22:30816200-30818200	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr22:30816200-30818400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr22:30816200-30818400	Enhancers	Psoas Muscle	Psoas
49	chr22:30816200-30818600	Genic enhancers	Brain Anterior Caudate	brain
50	chr22:30816200-30818600	Genic enhancers	Brain Inferior Temporal Lobe	brain

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