Variant report

Variant	rs5997959
Chromosome Location	chr22:31744072-31744073
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F6	chr22:31743281-31744088	H1-hESC	embryonic stem cell:	n/a	chr22:31743468-31743478 chr22:31743483-31743495 chr22:31743664-31743679
2	MAX	chr22:31742670-31744105	HepG2	liver:	n/a	chr22:31743680-31743689 chr22:31743707-31743716
3	POLR2A	chr22:31741151-31744106	H1-hESC	embryonic stem cell:	n/a	n/a
4	MTA3	chr22:31742647-31744163	GM12878	blood:	n/a	n/a
5	POLR2A	chr22:31742687-31744115	GM12892	blood:	n/a	n/a
6	POLR2A	chr22:31744067-31744073	MCF-7	breast:	n/a	n/a
7	SIN3AK20	chr22:31741116-31744158	MCF-7	breast:	n/a	n/a
8	POLR2A	chr22:31737335-31744213	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr22:31742630-31744081	HepG2	liver:	n/a	n/a
10	POLR2A	chr22:31738110-31744074	ECC-1	luminal epithelium:	n/a	n/a
11	POLR2A	chr22:31739924-31744267	HepG2	liver:	n/a	n/a
12	MAX	chr22:31739223-31744088	MCF-7	breast:	n/a	chr22:31743680-31743689 chr22:31742542-31742552 chr22:31741597-31741607 chr22:31739995-31740004 chr22:31741628-31741638 chr22:31741801-31741811 chr22:31742595-31742605 chr22:31743707-31743716 chr22:31741681-31741697
13	E2F6	chr22:31742677-31744164	H1-hESC	embryonic stem cell:	n/a	chr22:31743468-31743478 chr22:31743483-31743495 chr22:31743664-31743679
14	TCF12	chr22:31742048-31744165	A549	lung:	n/a	chr22:31743097-31743107
15	POLR2A	chr22:31742648-31744194	SK-N-MC	brain:	n/a	n/a
16	POLR2A	chr22:31741632-31744073	HEK293	kidney:	n/a	n/a
17	MAX	chr22:31741357-31744098	HepG2	liver:	n/a	chr22:31743680-31743689 chr22:31742542-31742552 chr22:31741597-31741607 chr22:31741628-31741638 chr22:31741801-31741811 chr22:31742595-31742605 chr22:31743707-31743716 chr22:31741681-31741697
18	POLR2A	chr22:31742646-31744074	GM12892	blood:	n/a	n/a
19	MAX	chr22:31742677-31744148	HCT-116	colon:	n/a	chr22:31743680-31743689 chr22:31743707-31743716
20	POLR2A	chr22:31738209-31744086	HL-60	blood:	n/a	n/a
21	MXI1	chr22:31739108-31744171	SK-N-SH	brain:	n/a	n/a
22	PML	chr22:31740884-31744165	GM12878	blood:	n/a	n/a
23	POLR2A	chr22:31741581-31744087	HL-60	blood:	n/a	n/a
24	POLR2A	chr22:31742620-31744074	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:31738670..31747056-chr22:31790500..31799012,36	MCF-7	breast:
2	chr22:31737798..31746418-chr22:31793074..31801662,34	MCF-7	breast:
3	chr10:74033244..74035559-chr22:31742440..31745127,2	MCF-7	breast:
4	chr22:31742672..31744282-chr22:31844664..31847017,2	MCF-7	breast:
5	chr22:31684664..31691252-chr22:31735490..31744100,29	MCF-7	breast:
6	chr22:31683915..31694680-chr22:31733392..31744713,34	MCF-7	breast:
7	chr22:31602004..31608593-chr22:31739507..31744494,7	MCF-7	breast:
8	chr22:31696471..31699232-chr22:31743755..31746050,2	MCF-7	breast:

Variant related genes	Relation type
PATZ1	TF binding region
ENSG00000100100	Chromatin interaction
ENSG00000168209	Chromatin interaction
ENSG00000182541	Chromatin interaction
ENSG00000184708	Chromatin interaction
ENSG00000185721	Chromatin interaction
ENSG00000228839	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs11089493	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11089495	1.00[CEU][hapmap];0.84[GIH][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs11089496	0.83[EUR][1000 genomes]
rs1123705	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs1138706	0.83[EUR][1000 genomes]
rs11556237	0.87[CEU][hapmap];0.81[TSI][hapmap]
rs11703005	0.87[CEU][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs11703576	0.83[EUR][1000 genomes]
rs11704523	0.87[CEU][hapmap];0.85[TSI][hapmap]
rs12157877	1.00[CEU][hapmap]
rs12165685	0.83[ASN][1000 genomes]
rs16989469	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs17220418	0.81[CHB][hapmap];0.85[ASN][1000 genomes]
rs17820958	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1859677	0.90[ASN][1000 genomes]
rs2057951	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2073856	0.86[CHB][hapmap];0.80[CHD][hapmap];0.86[JPT][hapmap]
rs2073859	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2073860	0.91[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap]
rs2073861	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs2144387	0.80[CEU][hapmap]
rs2158779	0.85[ASN][1000 genomes]
rs2240424	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2240427	0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2267168	0.86[CHB][hapmap];0.80[CHD][hapmap];0.95[JPT][hapmap]
rs2283882	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs2899161	0.94[CEU][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3091392	0.87[CEU][hapmap];0.81[TSI][hapmap]
rs4293639	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55837074	0.87[EUR][1000 genomes]
rs56292834	0.84[EUR][1000 genomes]
rs5749222	0.86[JPT][hapmap]
rs5749225	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs5749236	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs5749240	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs5749247	0.81[ASN][1000 genomes]
rs5749252	0.90[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs5749255	0.91[CHB][hapmap];0.80[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs5749257	0.89[ASN][1000 genomes]
rs5749258	0.87[ASN][1000 genomes]
rs5749262	0.81[ASN][1000 genomes]
rs5753485	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs5753494	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs5753495	0.93[JPT][hapmap]
rs5753509	0.81[JPT][hapmap]
rs5753511	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs5753516	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs5753519	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs5753523	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5753525	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs5753526	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs5753527	0.86[CHB][hapmap];0.80[CHD][hapmap];0.95[JPT][hapmap]
rs5753535	0.86[CHB][hapmap];0.80[CHD][hapmap];0.95[JPT][hapmap]
rs5753540	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs5753542	0.81[ASN][1000 genomes]
rs5753554	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5753555	0.86[ASN][1000 genomes]
rs5753556	0.86[ASN][1000 genomes]
rs5753561	0.86[ASN][1000 genomes]
rs5753566	0.91[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs5753569	0.90[ASN][1000 genomes]
rs5753571	0.89[ASN][1000 genomes]
rs5753572	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs5753574	0.91[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs5753683	0.80[CEU][hapmap]
rs5994386	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5994387	0.96[EUR][1000 genomes]
rs5997893	0.82[JPT][hapmap]
rs5997917	0.93[CEU][hapmap]
rs5997921	0.94[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5997924	0.88[EUR][1000 genomes]
rs5997937	1.00[CEU][hapmap];0.84[GIH][hapmap];0.92[TSI][hapmap]
rs5997942	0.93[CEU][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs5997948	0.91[EUR][1000 genomes]
rs5997956	0.96[EUR][1000 genomes]
rs5997965	0.94[EUR][1000 genomes]
rs60459126	0.90[EUR][1000 genomes]
rs695455	0.87[CEU][hapmap];0.81[TSI][hapmap]
rs695682	0.87[CEU][hapmap]
rs713619	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7286926	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7287715	0.87[CEU][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs7292620	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs739428	0.87[CEU][hapmap]
rs8135417	0.86[JPT][hapmap]
rs8143159	0.87[CEU][hapmap];0.85[TSI][hapmap]
rs8595	0.93[CEU][hapmap]
rs874356	0.86[JPT][hapmap]
rs9609263	0.88[LWK][hapmap];0.88[MKK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs9619178	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs9621212	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs9621226	0.81[ASN][1000 genomes]
rs9621236	0.82[ASN][1000 genomes]
rs9680708	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][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	nsv834176	chr22:31682426-31864701	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
2	esv3333136	chr22:31704947-31758417	Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers 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	28 gene(s)	inside rSNPs	diseases
3	esv1816779	chr22:31743711-31797094	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs5997959	DUSP18	cis	cerebellum	SCAN
rs5997959	SFI1	cis	cerebellum	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31740000-31744200	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr22:31741000-31744200	Active TSS	H9 Cell Line	embryonic stem cell
3	chr22:31741200-31744200	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr22:31741200-31744200	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr22:31741200-31744200	Active TSS	Colon Smooth Muscle	Colon
6	chr22:31741200-31744200	Active TSS	Fetal Brain Female	brain
7	chr22:31741600-31744200	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr22:31742800-31744200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
9	chr22:31742800-31744200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
10	chr22:31742800-31744200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr22:31742800-31744200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr22:31743200-31744200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr22:31743400-31744200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
14	chr22:31743400-31744200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr22:31743400-31744200	Flanking Active TSS	Dnd41	blood
16	chr22:31743600-31744200	Enhancers	Spleen	Spleen
17	chr22:31743800-31744200	Flanking Active TSS	Hela-S3	cervix
18	chr22:31744000-31744200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr22:31744000-31744200	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr22:31744000-31744200	Enhancers	Primary T cells fromperipheralblood	blood
21	chr22:31744000-31744200	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr22:31744000-31744200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr22:31744000-31744200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr22:31744000-31744200	Enhancers	Adipose Nuclei	Adipose
25	chr22:31744000-31744200	Enhancers	Liver	Liver
26	chr22:31744000-31744200	Active TSS	Brain Germinal Matrix	brain
27	chr22:31744000-31744200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr22:31744000-31744200	Enhancers	Colonic Mucosa	Colon
29	chr22:31744000-31744200	Enhancers	Duodenum Mucosa	Duodenum
30	chr22:31744000-31744200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr22:31744000-31744200	Enhancers	Fetal Brain Male	brain
32	chr22:31744000-31744200	Enhancers	Fetal Heart	heart
33	chr22:31744000-31744200	Enhancers	Fetal Intestine Large	intestine
34	chr22:31744000-31744200	Enhancers	Fetal Intestine Small	intestine
35	chr22:31744000-31744200	Enhancers	Fetal Muscle Trunk	muscle
36	chr22:31744000-31744200	Enhancers	Fetal Muscle Leg	muscle
37	chr22:31744000-31744200	Enhancers	Placenta	Placenta
38	chr22:31744000-31744200	Enhancers	Fetal Stomach	stomach
39	chr22:31744000-31744200	Active TSS	Rectal Mucosa Donor 31	rectum
40	chr22:31744000-31744200	Active TSS	Stomach Smooth Muscle	stomach
41	chr22:31744000-31744200	Enhancers	GM12878-XiMat	blood
42	chr22:31744000-31744200	Flanking Active TSS	HepG2	liver
43	chr22:31744000-31744200	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr22:31744000-31744200	Enhancers	NHDF-Ad	bronchial
45	chr22:31744000-31744400	Enhancers	Pancreas	Pancrea
46	chr22:31744000-31744800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr22:31744000-31745000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr22:31744000-31745000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr22:31744000-31745000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr22:31744000-31745800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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