Variant report

Variant	rs7290469
Chromosome Location	chr22:22150982-22150983
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:22145100..22147848-chr22:22150073..22153160,3	K562	blood:
2	chr22:22150579..22153553-chr22:22290936..22295210,3	K562	blood:
3	chr22:22149608..22152271-chr22:22219755..22223079,3	MCF-7	breast:
4	chr22:22149149..22152103-chr22:22281667..22284130,2	K562	blood:
5	chr22:22139542..22142043-chr22:22149818..22151655,3	K562	blood:
6	chr22:22144744..22147621-chr22:22148785..22151318,2	K562	blood:
7	chr22:22139792..22142043-chr22:22150140..22151655,2	K562	blood:
8	chr22:22118830..22121032-chr22:22149078..22151242,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000200985	Chromatin interaction
ENSG00000100034	Chromatin interaction
ENSG00000100030	Chromatin interaction
ENSG00000224086	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1063311	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11490038	0.83[EUR][1000 genomes]
rs11912377	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11913721	0.92[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13056532	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2266966	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2266969	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2283791	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2283793	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28566555	0.82[EUR][1000 genomes]
rs28697123	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28720995	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2876981	0.81[CEU][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs34550586	0.89[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4640486	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56036797	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56227348	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56398890	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5999749	0.93[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5999752	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62235132	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62235149	0.81[EUR][1000 genomes]
rs6518968	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7292584	0.80[EUR][1000 genomes]
rs8138075	0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8139376	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9340	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs9607241	1.00[CEU][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9607285	1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9607298	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9607320	0.82[ASN][1000 genomes]
rs9610271	0.85[CEU][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs9610294	0.85[ASN][1000 genomes]
rs9610314	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9610328	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9610338	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9610371	0.84[ASN][1000 genomes]
rs9610374	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9610375	0.82[CEU][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9610400	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948603	chr22:21928916-22601814	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	422 gene(s)	inside rSNPs	diseases
2	nsv948902	chr22:21928916-22657900	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	426 gene(s)	inside rSNPs	diseases
3	nsv1063962	chr22:21939722-22934593	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	477 gene(s)	inside rSNPs	diseases
4	nsv1058617	chr22:21939922-22934454	Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh 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	477 gene(s)	inside rSNPs	diseases
5	nsv529694	chr22:21957411-22905068	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	474 gene(s)	inside rSNPs	diseases
6	nsv531797	chr22:21977700-22959729	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	476 gene(s)	inside rSNPs	diseases
7	nsv1066403	chr22:22010822-22352262	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
8	nsv1066964	chr22:22055123-22228745	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv544604	chr22:22055123-22228745	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv588322	chr22:22086373-22186479	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
11	nsv948580	chr22:22100718-22839559	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
12	esv1795495	chr22:22131125-22204916	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv914470	chr22:22131125-22272737	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
14	nsv1059265	chr22:22131125-22457154	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer 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 miRNA target site	47 gene(s)	inside rSNPs	diseases
15	esv3379268	chr22:22135347-22446281	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer 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	47 gene(s)	inside rSNPs	diseases
16	esv3385441	chr22:22135777-22320294	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
17	esv2752404	chr22:22141825-22570417	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
18	esv2422277	chr22:22144108-22442159	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS 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	47 gene(s)	inside rSNPs	diseases
19	esv2422295	chr22:22144108-22442159	Bivalent/Poised TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs7290469	TOP3B	cis	parietal	SCAN
rs7290469	psiTPTE22	cis	parietal	SCAN
rs7290469	LL22NC03-86G7.1	cis	Thyroid	GTEx
rs7290469	DGCR6	cis	cerebellum	SCAN
rs7290469	TSSK2	cis	parietal	SCAN
rs7290469	USP18	cis	cerebellum	SCAN
rs7290469	LZTR1	cis	cerebellum	SCAN
rs7290469	UFD1L	cis	cerebellum	SCAN
rs7290469	LL22NC03-86G7.1	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:22113400-22163800	Weak transcription	Right Atrium	heart
2	chr22:22114200-22172800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr22:22121600-22171400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr22:22123200-22162200	Strong transcription	Fetal Thymus	thymus
5	chr22:22127200-22167600	Weak transcription	Psoas Muscle	Psoas
6	chr22:22127200-22170600	Weak transcription	Hela-S3	cervix
7	chr22:22129000-22162200	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr22:22129600-22151200	Weak transcription	Colon Smooth Muscle	Colon
9	chr22:22129800-22152000	Weak transcription	Brain Germinal Matrix	brain
10	chr22:22132000-22152000	Weak transcription	Right Ventricle	heart
11	chr22:22133400-22156000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr22:22134200-22162200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr22:22134600-22151200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr22:22135200-22152400	Strong transcription	Fetal Muscle Trunk	muscle
15	chr22:22135200-22162200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr22:22135800-22162400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr22:22135800-22162600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr22:22135800-22162600	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr22:22136000-22162400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr22:22136200-22161800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr22:22137600-22152400	Weak transcription	Esophagus	oesophagus
22	chr22:22137600-22162600	Strong transcription	Dnd41	blood
23	chr22:22138400-22152000	Weak transcription	Spleen	Spleen
24	chr22:22139200-22172800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr22:22139400-22151800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr22:22139600-22154600	Weak transcription	Fetal Brain Male	brain
27	chr22:22139800-22151200	Weak transcription	Pancreas	Pancrea
28	chr22:22140800-22161800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr22:22141000-22151200	Strong transcription	Fetal Muscle Leg	muscle
30	chr22:22141000-22162000	Strong transcription	Fetal Intestine Large	intestine
31	chr22:22141000-22162200	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr22:22142600-22151000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr22:22142800-22170600	Weak transcription	Colonic Mucosa	Colon
34	chr22:22143200-22152400	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr22:22143200-22155000	Weak transcription	Aorta	Aorta
36	chr22:22143800-22151200	Weak transcription	Primary hematopoietic stem cells	blood
37	chr22:22144000-22154400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr22:22144200-22151400	Strong transcription	Fetal Stomach	stomach
39	chr22:22144400-22160200	Strong transcription	Fetal Intestine Small	intestine
40	chr22:22145200-22162200	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr22:22145600-22152000	Weak transcription	Left Ventricle	heart
42	chr22:22145800-22170600	Weak transcription	Small Intestine	intestine
43	chr22:22146000-22162000	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr22:22146200-22152000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr22:22146200-22152200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr22:22146400-22162200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr22:22146600-22151800	Weak transcription	Stomach Mucosa	stomach
48	chr22:22146600-22151800	Weak transcription	GM12878-XiMat	blood
49	chr22:22146600-22152200	Weak transcription	HSMMtube	muscle
50	chr22:22146600-22152200	Weak transcription	NH-A	brain

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