Variant report

Variant	rs7290696
Chromosome Location	chr22:32341684-32341685
allele	C/T
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:27)
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	chr22:32339741-32341730	Hela-S3	cervix:	n/a	n/a
2	MXI1	chr22:32339474-32343821	SK-N-SH	brain:	n/a	n/a
3	MXI1	chr22:32339679-32342128	GM12878	blood:	n/a	n/a
4	POLR2A	chr22:32339465-32342192	Hela-S3	cervix:	n/a	n/a
5	ELK1	chr22:32341526-32341785	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr22:32339598-32341842	HL-60	blood:	n/a	n/a
7	POLR2A	chr22:32339500-32342859	K562	blood:	n/a	n/a
8	POLR2A	chr22:32339606-32345108	IMR90	lung:	n/a	n/a
9	ELK1	chr22:32341478-32341830	GM12878	blood:	n/a	n/a
10	MAX	chr22:32339607-32341782	Hela-S3	cervix:	n/a	chr22:32340069-32340076 chr22:32340395-32340405
11	POLR2A	chr22:32339690-32341711	GM15510	blood:	n/a	n/a
12	POLR2A	chr22:32339683-32342704	H1-neurons	neurons:	n/a	n/a
13	POLR2A	chr22:32339453-32341900	K562	blood:	n/a	n/a
14	POLR2A	chr22:32339641-32341962	H1-neurons	neurons:	n/a	n/a
15	CHD1	chr22:32341164-32342085	H1-hESC	embryonic stem cell:	n/a	n/a
16	BHLHE40	chr22:32341194-32341739	GM12878	blood:	n/a	n/a
17	POLR2A	chr22:32339552-32341882	HepG2	liver:	n/a	n/a
18	POLR2A	chr22:32339427-32342832	K562	blood:	n/a	n/a
19	POLR2A	chr22:32341570-32342133	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr22:32339723-32341794	GM19193	blood:	n/a	n/a
21	MAZ	chr22:32339487-32342007	IMR90	lung:	n/a	chr22:32340069-32340076 chr22:32340395-32340405
22	POLR2A	chr22:32341088-32341810	GM12892	blood:	n/a	n/a
23	POLR2A	chr22:32339651-32343721	K562	blood:	n/a	n/a
24	POLR2A	chr22:32339736-32341687	GM12878	blood:	n/a	n/a
25	POLR2A	chr22:32341627-32345124	HepG2	liver:	n/a	n/a
26	POLR2A	chr22:32339495-32341733	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr22:32341357-32341694	MCF-7	breast:	n/a	n/a
28	SIN3A	chr22:32339728-32341703	H1-hESC	embryonic stem cell:	n/a	chr22:32340042-32340053
29	RUNX3	chr22:32341365-32341883	GM12878	blood:	n/a	n/a
30	MXI1	chr22:32339732-32341832	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr22:32339674-32341695	HUVEC	blood vessel:	n/a	n/a
32	IRF1	chr22:32341647-32342040	K562	blood:	n/a	n/a
33	POLR2A	chr22:32341158-32342857	HepG2	liver:	n/a	n/a
34	REST	chr22:32339423-32342896	H1-neurons	neurons:	n/a	chr22:32340395-32340408 chr22:32340642-32340652 chr22:32340411-32340421
35	MAX	chr22:32339629-32341707	NB4	blood:	n/a	chr22:32340069-32340076 chr22:32340395-32340405
36	TAF1	chr22:32339892-32341773	H1-neurons	neurons:	n/a	n/a
37	POLR2A	chr22:32339677-32341738	GM18526	blood:	n/a	n/a
38	RAD21	chr22:32338914-32343861	SK-N-SH	brain:	n/a	n/a
39	MAZ	chr22:32339986-32341904	GM12878	blood:	n/a	chr22:32340069-32340076 chr22:32340395-32340405
40	POLR2A	chr22:32339638-32342411	Hela-S3	cervix:	n/a	n/a
41	MTA3	chr22:32340934-32342133	GM12878	blood:	n/a	n/a
42	ELF1	chr22:32341469-32341706	K562	blood:	n/a	n/a
43	POLR2A	chr22:32341677-32342856	MCF10A-Er-Src	breast:	n/a	n/a
44	POLR2A	chr22:32339487-32341914	H1-hESC	embryonic stem cell:	n/a	n/a
45	MXI1	chr22:32339637-32341755	HepG2	liver:	n/a	n/a
46	BHLHE40	chr22:32341260-32341838	K562	blood:	n/a	n/a
47	POLR2A	chr22:32339732-32342841	GM12878	blood:	n/a	n/a
48	POLR2A	chr22:32339785-32341789	GM19099	blood:	n/a	n/a
49	RCOR1	chr22:32341160-32341722	Hela-S3	cervix:	n/a	n/a
50	POLR2A	chr22:32340955-32341989	SK-N-MC	brain:	n/a	n/a

No data

(count:27 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:32148473..32152307-chr22:32339145..32342092,6	K562	blood:
2	chr22:32287695..32295635-chr22:32339159..32346051,14	K562	blood:
3	chr22:32058182..32059714-chr22:32339404..32341859,2	MCF-7	breast:
4	chr22:32143401..32146678-chr22:32340513..32343465,3	K562	blood:
5	chr22:32290403..32295434-chr22:32338835..32345403,11	K562	blood:
6	22:31829733-31836635..22:32338420-32342898	K562	blood:
7	chr22:32340518..32342759-chr22:32869952..32872764,2	K562	blood:
8	chr22:32213023..32215994-chr22:32340622..32343238,2	MCF-7	breast:
9	chr22:32265561..32271092-chr22:32337255..32342585,8	MCF-7	breast:
10	chr22:32329388..32335571-chr22:32336708..32343906,17	K562	blood:
11	chr22:32263494..32270321-chr22:32339054..32343535,9	K562	blood:
12	chr22:32055976..32060358-chr22:32339389..32343294,9	K562	blood:
13	chr22:32340998..32345394-chr22:32364660..32368897,5	MCF-7	breast:
14	chr22:32287148..32289580-chr22:32339395..32341919,4	K562	blood:
15	chr22:32264603..32274220-chr22:32339477..32348693,21	K562	blood:
16	chr22:32333714..32338666-chr22:32338808..32341895,4	MCF-7	breast:
17	chr22:32148601..32151339-chr22:32339160..32341973,3	MCF-7	breast:
18	chr22:31884354..31887535-chr22:32340375..32343416,3	MCF-7	breast:
19	22:31936958-31958600..22:32338420-32342898	K562	blood:
20	chr22:32147800..32152307-chr22:32338859..32342135,7	K562	blood:
21	chr22:32267945..32270075-chr22:32339613..32341959,2	MCF-7	breast:
22	chr22:32054689..32061174-chr22:32339137..32344183,9	K562	blood:
23	chr22:32142746..32147740-chr22:32340513..32344780,7	K562	blood:
24	chr22:32149264..32152111-chr22:32339608..32342388,3	MCF-7	breast:
25	chr22:32023093..32026034-chr22:32340368..32341945,2	K562	blood:
26	22:32284948-32287956..22:32338420-32342898	Hela-S3	cervix:
27	22:32150875-32154575..22:32338420-32342898	K562	blood:

No data

Variant related genes	Relation type
YWHAH	TF binding region
C22orf24	TF binding region
ENSG00000100150	Chromatin interaction
ENSG00000214093	Chromatin interaction
ENSG00000236132	Chromatin interaction
ENSG00000230866	Chromatin interaction
ENSG00000183530	Chromatin interaction
ENSG00000241878	Chromatin interaction
ENSG00000227813	Chromatin interaction
ENSG00000100225	Chromatin interaction
ENSG00000242251	Chromatin interaction
ENSG00000184708	Chromatin interaction
ENSG00000198089	Chromatin interaction
ENSG00000128254	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1049583	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap]
rs12168840	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs130256	0.81[MEX][hapmap]
rs130264	0.81[MEX][hapmap]
rs2246704	0.88[CHB][hapmap]
rs2301415	0.95[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs2853884	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs2853887	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs2858750	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs2858752	0.88[CHB][hapmap]
rs4820059	0.88[CHB][hapmap];0.83[CHD][hapmap];1.00[YRI][hapmap]
rs6518758	0.81[MEX][hapmap]
rs71806276	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7291050	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7364274	0.90[CEU][hapmap];1.00[LWK][hapmap]
rs738181	1.00[ASW][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.88[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs8141011	0.95[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs933226	1.00[CHB][hapmap];0.88[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs9606887	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9606888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9606893	0.81[MEX][hapmap]
rs9606907	0.81[MEX][hapmap]
rs9609389	1.00[ASW][hapmap]
rs9609394	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap]
rs9609396	0.86[CHB][hapmap];0.84[CHD][hapmap];0.81[MEX][hapmap]
rs9609397	1.00[YRI][hapmap]
rs9621371	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9621373	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9621386	0.81[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428046	chr22:32316302-32356963	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	esv3443461	chr22:32339402-32341825	Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Weak transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7290696	TUG1	cis	cerebellum	SCAN
rs7290696	CCDC117	cis	cerebellum	SCAN
rs7290696	LIF	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:32339600-32342000	Active TSS	Duodenum Smooth Muscle	Duodenum
2	chr22:32339600-32342400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr22:32339600-32342400	Active TSS	Brain Angular Gyrus	brain
4	chr22:32339600-32342600	Active TSS	H9 Cell Line	embryonic stem cell
5	chr22:32339600-32342800	Active TSS	Psoas Muscle	Psoas
6	chr22:32339600-32343200	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr22:32339600-32343600	Active TSS	Aorta	Aorta
8	chr22:32339600-32343600	Active TSS	Right Atrium	heart
9	chr22:32339800-32341800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr22:32339800-32341800	Active TSS	Sigmoid Colon	Sigmoid Colon
11	chr22:32339800-32341800	Active TSS	Small Intestine	intestine
12	chr22:32339800-32342000	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr22:32339800-32342000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr22:32339800-32342000	Active TSS	Left Ventricle	heart
15	chr22:32339800-32342200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr22:32339800-32342200	Active TSS	Ovary	ovary
17	chr22:32339800-32342600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr22:32339800-32342600	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr22:32339800-32343400	Active TSS	Lung	lung
20	chr22:32340000-32341800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr22:32340000-32341800	Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr22:32340000-32341800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr22:32340000-32341800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr22:32340000-32341800	Active TSS	Esophagus	oesophagus
25	chr22:32340000-32341800	Active TSS	Rectal Smooth Muscle	rectum
26	chr22:32340000-32341800	Active TSS	GM12878-XiMat	blood
27	chr22:32340000-32341800	Active TSS	Hela-S3	cervix
28	chr22:32340000-32342000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr22:32340000-32342000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr22:32340000-32342000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
31	chr22:32340000-32342000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr22:32340000-32342000	Active TSS	Brain Germinal Matrix	brain
33	chr22:32340000-32342000	Active TSS	Colonic Mucosa	Colon
34	chr22:32340000-32342000	Active TSS	Fetal Muscle Trunk	muscle
35	chr22:32340000-32342000	Active TSS	Gastric	stomach
36	chr22:32340000-32342000	Active TSS	Right Ventricle	heart
37	chr22:32340000-32342000	Active TSS	NHDF-Ad	bronchial
38	chr22:32340000-32342000	Active TSS	NHLF	lung
39	chr22:32340000-32342200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr22:32340000-32342200	Active TSS	Pancreas	Pancrea
41	chr22:32340000-32342400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr22:32340000-32342400	Active TSS	Fetal Intestine Large	intestine
43	chr22:32340000-32342800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr22:32340400-32342400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr22:32341000-32341800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
46	chr22:32341000-32341800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
47	chr22:32341000-32341800	Active TSS	Fetal Heart	heart
48	chr22:32341000-32342000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
49	chr22:32341000-32342000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
50	chr22:32341000-32342000	Flanking Active TSS	Primary B cells from cord blood	blood

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