Variant report

Variant	rs2072158
Chromosome Location	chr22:30822461-30822462
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:201)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:201 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr22:30822460-30822843	GM12892	blood:	n/a	n/a
2	CTCF	chr22:30822382-30822784	K562	blood:	n/a	n/a
3	MAX	chr22:30821497-30822933	ECC-1	luminal epithelium:	n/a	n/a
4	MYC	chr22:30822377-30822760	H1-hESC	embryonic stem cell:	n/a	n/a
5	CHD2	chr22:30821509-30822890	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr22:30821574-30822903	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr22:30820904-30822814	HUVEC	blood vessel:	n/a	n/a
8	CTCF	chr22:30822360-30822510	MCF-7	breast:	n/a	n/a
9	MAZ	chr22:30818156-30822979	IMR90	lung:	n/a	n/a
10	MYC	chr22:30821491-30822750	K562	blood:	n/a	n/a
11	RAD21	chr22:30822451-30822824	HepG2	liver:	n/a	n/a
12	NR2F2	chr22:30821482-30822906	MCF-7	breast:	n/a	n/a
13	CHD2	chr22:30821535-30823010	GM12878	blood:	n/a	n/a
14	TFAP2C	chr22:30821513-30822968	Hela-S3	cervix:	n/a	chr22:30822693-30822708
15	POLR2A	chr22:30818871-30822893	MCF10A-Er-Src	breast:	n/a	n/a
16	MAX	chr22:30821323-30823007	A549	lung:	n/a	n/a
17	POLR2A	chr22:30818645-30822915	Hela-S3	cervix:	n/a	n/a
18	REST	chr22:30822214-30822628	A549	lung:	n/a	n/a
19	CTCF	chr22:30822455-30822806	A549	lung:	n/a	n/a
20	RUNX3	chr22:30822198-30822834	GM12878	blood:	n/a	n/a
21	CTCF	chr22:30822424-30822863	H1-hESC	embryonic stem cell:	n/a	n/a
22	ZNF143	chr22:30822408-30822808	K562	blood:	n/a	n/a
23	SIN3A	chr22:30821427-30822885	H1-hESC	embryonic stem cell:	n/a	n/a
24	RUNX3	chr22:30821410-30822824	GM12878	blood:	n/a	n/a
25	RAD21	chr22:30822420-30822821	SK-N-SH_RA	brain:	n/a	n/a
26	POLR2A	chr22:30817509-30822980	HUVEC	blood vessel:	n/a	n/a
27	MYC	chr22:30821531-30822894	MCF10A-Er-Src	breast:	n/a	n/a
28	CHD1	chr22:30816159-30822993	IMR90	lung:	n/a	n/a
29	ATF2	chr22:30822336-30822844	H1-hESC	embryonic stem cell:	n/a	n/a
30	YY1	chr22:30822255-30822852	GM12878	blood:	n/a	n/a
31	NFIC	chr22:30822430-30822746	HepG2	liver:	n/a	n/a
32	BCLAF1	chr22:30822235-30822865	GM12878	blood:	n/a	n/a
33	SMC3	chr22:30821471-30822907	SK-N-SH	brain:	n/a	n/a
34	POLR2A	chr22:30821601-30822741	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr22:30821465-30822902	GM12878	blood:	n/a	n/a
36	MAZ	chr22:30821486-30822873	GM12878	blood:	n/a	n/a
37	TCF12	chr22:30821393-30822937	A549	lung:	n/a	n/a
38	POLR2A	chr22:30821457-30822761	GM12892	blood:	n/a	n/a
39	POLR2A	chr22:30816245-30822974	PBDE	blood:	n/a	n/a
40	KAP1	chr22:30822353-30822723	U2OS	brain:	n/a	n/a
41	MAX	chr22:30821378-30822886	ECC-1	luminal epithelium:	n/a	n/a
42	EBF1	chr22:30822442-30822923	GM12878	blood:	n/a	n/a
43	POLR2A	chr22:30818136-30822953	HCT-116	colon:	n/a	n/a
44	RELA	chr22:30821480-30822846	GM19099	blood:	n/a	n/a
45	POLR2A	chr22:30821570-30822635	GM12878	blood:	n/a	n/a
46	RELA	chr22:30821544-30822792	GM18951	blood:	n/a	n/a
47	NFYB	chr22:30822158-30822751	Hela-S3	cervix:	n/a	chr22:30822310-30822320 chr22:30822468-30822482 chr22:30822308-30822322 chr22:30822309-30822324 chr22:30822307-30822322 chr22:30822470-30822480
48	MYC	chr22:30822456-30822918	HUVEC	blood vessel:	n/a	n/a
49	KAP1	chr22:30821520-30822791	HEK293	kidney:	n/a	n/a
50	ZKSCAN1	chr22:30822449-30822832	Hela-S3	cervix:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:30821810..30824396-chr22:30842591..30845035,2	K562	blood:
2	chr22:30814763..30819112-chr22:30819393..30823307,5	MCF-7	breast:
3	chr22:30803275..30806677-chr22:30820826..30824180,3	MCF-7	breast:
4	chr22:30787202..30787778-chr22:30822213..30823130,2	MCF-7	breast:
5	chr22:30820440..30822751-chr22:31090157..31092444,2	MCF-7	breast:
6	chr12:57480730..57482980-chr22:30821436..30824082,2	MCF-7	breast:
7	chr22:30816361..30822733-chr22:30829064..30833429,8	K562	blood:
8	chr22:30786847..30787701-chr22:30822197..30822724,2	K562	blood:
9	chr22:30822226..30822902-chr5:1345317..1345847,2	Hela-S3	cervix:
10	chr22:30684393..30686613-chr22:30820961..30823363,3	MCF-7	breast:
11	chr22:30821507..30822491-chr5:68462804..68463489,2	Hela-S3	cervix:
12	chr22:30691985..30694269-chr22:30820626..30822582,2	MCF-7	breast:
13	chr22:30786785..30787943-chr22:30821846..30823177,6	MCF-7	breast:
14	chr22:30821818..30823815-chr22:30836918..30838469,2	K562	blood:
15	chr22:30787731..30797808-chr22:30813672..30825727,31	MCF-7	breast:
16	chr19:1438390..1438932-chr22:30821695..30822570,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
RNF215	TF binding region
ENSG00000272689	TF binding region
ENSG00000184792	Chromatin interaction
ENSG00000166881	Chromatin interaction
ENSG00000272689	Chromatin interaction
ENSG00000203606	Chromatin interaction
ENSG00000115268	Chromatin interaction
ENSG00000099992	Chromatin interaction
ENSG00000100003	Chromatin interaction
ENSG00000239282	Chromatin interaction
ENSG00000273350	Chromatin interaction
ENSG00000166886	Chromatin interaction
ENSG00000134057	Chromatin interaction
ENSG00000222915	Chromatin interaction
ENSG00000099999	Chromatin interaction
ENSG00000249590	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1061660	1.00[ASW][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1061664	0.89[MEX][hapmap]
rs12106618	0.83[AFR][1000 genomes]
rs16988620	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2018514	0.91[AFR][1000 genomes]
rs2072157	1.00[ASW][hapmap];0.95[LWK][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes]
rs2072159	0.86[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2074651	0.92[YRI][hapmap];0.91[AFR][1000 genomes]
rs2283868	0.91[AFR][1000 genomes]
rs2283869	0.93[AFR][1000 genomes]
rs28523826	0.90[AFR][1000 genomes]
rs4820010	0.90[AFR][1000 genomes]
rs5753117	0.87[ASW][hapmap];0.95[LWK][hapmap];0.89[MEX][hapmap];0.95[MKK][hapmap]
rs5997629	0.93[ASW][hapmap];0.95[LWK][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes]
rs5997641	1.00[ASW][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes]
rs7292744	0.90[AFR][1000 genomes]
rs73390209	0.87[AFR][1000 genomes]
rs757660	0.89[MEX][hapmap];0.80[MKK][hapmap]
rs887098	0.81[AFR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2072158	PATZ1	cis	parietal	SCAN
rs2072158	LIF	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30818600-30822600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr22:30818600-30822600	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr22:30818600-30822800	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr22:30818600-30823000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr22:30818800-30822600	Active TSS	Psoas Muscle	Psoas
6	chr22:30819000-30822600	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr22:30819000-30822600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr22:30819000-30822800	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr22:30819200-30822600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr22:30819200-30823000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr22:30819400-30823200	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr22:30820000-30822600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
13	chr22:30820200-30822600	Flanking Active TSS	Liver	Liver
14	chr22:30820200-30822800	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr22:30820200-30822800	Flanking Active TSS	Primary B cells from peripheral blood	blood
16	chr22:30820200-30822800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr22:30820200-30822800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
18	chr22:30820200-30822800	Flanking Active TSS	NH-A	brain
19	chr22:30820200-30823000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
20	chr22:30820200-30823000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
21	chr22:30820200-30823200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
22	chr22:30820400-30822800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
23	chr22:30820400-30822800	Flanking Active TSS	Stomach Smooth Muscle	stomach
24	chr22:30820400-30823000	Flanking Active TSS	Duodenum Mucosa	Duodenum
25	chr22:30820600-30822600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
26	chr22:30820800-30823200	Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr22:30821200-30822600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr22:30821200-30822800	Active TSS	H1 Cell Line	embryonic stem cell
29	chr22:30821200-30822800	Active TSS	Brain Substantia Nigra	brain
30	chr22:30821200-30823000	Active TSS	H9 Cell Line	embryonic stem cell
31	chr22:30821200-30823000	Active TSS	Brain Anterior Caudate	brain
32	chr22:30821200-30823000	Active TSS	Rectal Smooth Muscle	rectum
33	chr22:30821400-30822600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr22:30821400-30822600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr22:30821400-30822600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
36	chr22:30821400-30822600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
37	chr22:30821400-30822600	Flanking Active TSS	Fetal Intestine Small	intestine
38	chr22:30821400-30822600	Flanking Active TSS	Fetal Muscle Leg	muscle
39	chr22:30821400-30822600	Flanking Active TSS	Placenta	Placenta
40	chr22:30821400-30822600	Flanking Active TSS	Fetal Thymus	thymus
41	chr22:30821400-30822800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr22:30821400-30822800	Flanking Active TSS	Adipose Nuclei	Adipose
43	chr22:30821400-30822800	Flanking Active TSS	Colonic Mucosa	Colon
44	chr22:30821400-30822800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
45	chr22:30821400-30822800	Flanking Active TSS	Fetal Muscle Trunk	muscle
46	chr22:30821400-30822800	Active TSS	Hela-S3	cervix
47	chr22:30821400-30823000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
48	chr22:30821400-30823000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
49	chr22:30821400-30823000	Flanking Active TSS	HMEC	breast
50	chr22:30821600-30822600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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