Variant report

Variant	rs5997893
Chromosome Location	chr22:31556103-31556104
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:445)
CpG islands
(count:183)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 1)
miRNA target
sites (count:0)

(count:445 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr22:31555872-31556485	H1-hESC	embryonic stem cell:	n/a	n/a
2	RFX5	chr22:31555989-31556267	GM12878	blood:	n/a	n/a
3	GTF2F1	chr22:31555951-31556274	Hela-S3	cervix:	n/a	n/a
4	YY1	chr22:31555866-31556309	GM12892	blood:	n/a	n/a
5	GTF2F1	chr22:31555921-31556271	H1-hESC	embryonic stem cell:	n/a	n/a
6	HEY1	chr22:31555913-31556290	HepG2	liver:	n/a	n/a
7	USF1	chr22:31555909-31556408	A549	lung:	n/a	n/a
8	RCOR1	chr22:31555857-31556328	K562	blood:	n/a	n/a
9	CTCF	chr22:31556000-31556150	HMEC	breast:	n/a	chr22:31556075-31556088
10	EGR1	chr22:31555992-31556363	K562	blood:	n/a	chr22:31556181-31556195 chr22:31556335-31556344 chr22:31556119-31556128 chr22:31556310-31556323 chr22:31556332-31556345
11	ATF3	chr22:31555987-31556303	HepG2	liver:	n/a	n/a
12	BCL3	chr22:31555844-31556326	A549	lung:	n/a	chr22:31556310-31556319
13	GABPA	chr22:31555874-31556326	HepG2	liver:	n/a	n/a
14	CREB1	chr22:31555940-31556305	A549	lung:	n/a	n/a
15	FOXA1	chr22:31556022-31556264	T-47D	breast:	n/a	n/a
16	ETS1	chr22:31555874-31556319	A549	lung:	n/a	chr22:31556130-31556145 chr22:31556130-31556143 chr22:31556117-31556128 chr22:31556130-31556143 chr22:31556066-31556077 chr22:31556134-31556144 chr22:31556133-31556142 chr22:31556120-31556129 chr22:31556121-31556130 chr22:31556133-31556142 chr22:31556133-31556150 chr22:31556131-31556140
17	USF1	chr22:31555795-31556504	SK-N-SH	brain:	n/a	n/a
18	GABPA	chr22:31555792-31556466	SK-N-SH	brain:	n/a	n/a
19	JUND	chr22:31555979-31556324	A549	lung:	n/a	n/a
20	EP300	chr22:31555911-31556345	HepG2	liver:	n/a	chr22:31556134-31556141
21	POLR2A	chr22:31555965-31556305	GM12878	blood:	n/a	n/a
22	MAX	chr22:31555891-31556342	SK-N-SH	brain:	n/a	n/a
23	GABPA	chr22:31555485-31556534	A549	lung:	n/a	n/a
24	POLR2A	chr22:31555907-31556383	HUVEC	blood vessel:	n/a	n/a
25	PBX3	chr22:31555919-31556477	SK-N-SH	brain:	n/a	n/a
26	TAF1	chr22:31555832-31556582	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr22:31555902-31556392	K562	blood:	n/a	n/a
28	TAF1	chr22:31555779-31556517	ECC-1	luminal epithelium:	n/a	n/a
29	POLR2A	chr22:31555851-31556531	GM12892	blood:	n/a	n/a
30	ELF1	chr22:31555924-31556296	MCF-7	breast:	n/a	chr22:31556118-31556131
31	POLR2A	chr22:31555957-31556350	SK-N-MC	brain:	n/a	n/a
32	ELF1	chr22:31555899-31556443	MCF-7	breast:	n/a	chr22:31556118-31556131
33	POU2F2	chr22:31555928-31556294	GM12878	blood:	n/a	n/a
34	POLR2A	chr22:31555836-31556617	MCF-7	breast:	n/a	n/a
35	POLR2A	chr22:31555854-31556424	GM19099	blood:	n/a	n/a
36	SIX5	chr22:31555927-31556275	A549	lung:	n/a	n/a
37	CTCF	chr22:31556020-31556170	BJ	skin:	n/a	chr22:31556075-31556088
38	NR2F2	chr22:31555843-31556417	MCF-7	breast:	n/a	n/a
39	CREB1	chr22:31555889-31556330	GM12878	blood:	n/a	n/a
40	POLR2A	chr22:31555918-31556364	PANC-1	pancreas:	n/a	n/a
41	POLR2A	chr22:31555659-31556440	Hela-S3	cervix:	n/a	n/a
42	YY1	chr22:31555873-31556293	SK-N-SH_RA	brain:	n/a	n/a
43	TBP	chr22:31555946-31556307	Hela-S3	cervix:	n/a	chr22:31556291-31556302
44	PBX3	chr22:31555942-31556534	SK-N-SH	brain:	n/a	n/a
45	POLR2A	chr22:31555855-31556353	HL-60	blood:	n/a	n/a
46	CEBPB	chr22:31556002-31556327	A549	lung:	n/a	n/a
47	YY1	chr22:31555867-31556265	GM12878	blood:	n/a	n/a
48	NFE2	chr22:31556008-31556293	GM12878	blood:	n/a	n/a
49	NFIC	chr22:31555860-31556308	HepG2	liver:	n/a	n/a
50	ATF3	chr22:31556007-31556251	K562	blood:	n/a	n/a

(count:183 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr22:31556080-31556130	NB4	blood:	n/a
2	chr22:31556069-31556119	HNPCEpiC	eye:	n/a
3	chr22:31556080-31556130	K562	blood:	n/a
4	chr22:31556086-31556136	H1-hESC	embryonic stem cell:	embryo
5	chr22:31556086-31556136	NHBE	bronchial:	n/a
6	chr22:31556080-31556130	NH-A	brain:	n/a
7	chr22:31556080-31556130	BE2_C	brain:	n/a
8	chr22:31556069-31556119	PrEC	prostate:	n/a
9	chr22:31556080-31556130	PrEC	prostate:	n/a
10	chr22:31556069-31556119	SK-N-MC	brain:	n/a
11	chr22:31556086-31556136	HCM	heart:	n/a
12	chr22:31556086-31556136	AoSMC	blood vessel:	n/a
13	chr22:31556069-31556119	HAEpiC	amniotic membrane:	n/a
14	chr22:31556080-31556130	GM12878	blood:	n/a
15	chr22:31556069-31556119	SK-N-SH	brain:	n/a
16	chr22:31556069-31556119	IMR90	lung:	fetal
17	chr22:31556069-31556119	AG10803	skin:	n/a
18	chr22:31556086-31556136	AG09319	gingival:	n/a
19	chr22:31556069-31556119	HCT-116	colon:	n/a
20	chr22:31556069-31556119	AG09309	skin:	n/a
21	chr22:31556080-31556130	HUVEC	blood vessel:	n/a
22	chr22:31556080-31556130	A549	lung:	n/a
23	chr22:31556086-31556136	CMK	blood:	n/a
24	chr22:31556069-31556119	SKMC	muscle:	n/a
25	chr22:31556086-31556136	HRCEpiC	kidney:	n/a
26	chr22:31556086-31556136	Hela-S3	cervix:	n/a
27	chr22:31556069-31556119	T-47D	breast:	n/a
28	chr22:31556080-31556130	GM12892	blood:	n/a
29	chr22:31556086-31556136	ECC-1	luminal epithelium:	n/a
30	chr22:31556069-31556119	HCPEpiC	choroid plexus:	n/a
31	chr22:31556069-31556119	H1-hESC	embryonic stem cell:	embryo
32	chr22:31556086-31556136	A549	lung:	n/a
33	chr22:31556080-31556130	ECC-1	luminal epithelium:	n/a
34	chr22:31556069-31556119	Jurkat	blood:	n/a
35	chr22:31556080-31556130	Jurkat	blood:	n/a
36	chr22:31556086-31556136	HUVEC	blood vessel:	n/a
37	chr22:31556069-31556119	HRCEpiC	kidney:	n/a
38	chr22:31556080-31556130	PFSK-1	brain:	n/a
39	chr22:31556086-31556136	HEEpiC	esophagus:	n/a
40	chr22:31556086-31556136	MCF-7	breast:	n/a
41	chr22:31556069-31556119	GM12878	blood:	n/a
42	chr22:31556080-31556130	HL-60	blood:	n/a
43	chr22:31556069-31556119	K562	blood:	n/a
44	chr22:31556086-31556136	GM12892	blood:	n/a
45	chr22:31556086-31556136	HMEC	breast:	n/a
46	chr22:31556069-31556119	SAEC	small airway:	n/a
47	chr22:31556086-31556136	GM12878	blood:	n/a
48	chr22:31556069-31556119	HPAEpiC	pulmonary alveolar:	n/a
49	chr22:31556080-31556130	NHBE	bronchial:	n/a
50	chr22:31556080-31556130	HAEpiC	amniotic membrane:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:31555142..31556725-chr22:31643704..31646530,2	MCF-7	breast:
2	chr22:31534966..31537778-chr22:31554685..31557531,2	MCF-7	breast:

No data

miRNA name	Chromosome Location	mirBase accession
hsa-miR-3928-5p	chr22:31556081-31556103	MIMAT0027037

No data

Variant related genes	Relation type
ENSG00000214125	TF binding region
RNF185	TF binding region
RNF185	CpG island
ENSG00000214125	CpG island
ENSG00000100078	Chromatin interaction
ENSG00000182541	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1034589	0.90[MEX][hapmap]
rs11089493	0.86[JPT][hapmap]
rs13158	0.90[MEX][hapmap]
rs17820958	0.82[JPT][hapmap]
rs1858821	0.90[MEX][hapmap]
rs2057951	0.82[JPT][hapmap]
rs2073856	0.86[JPT][hapmap]
rs2073857	0.90[MEX][hapmap]
rs2073859	0.86[JPT][hapmap]
rs2073860	0.86[JPT][hapmap]
rs2073861	0.86[JPT][hapmap]
rs2074734	0.81[JPT][hapmap]
rs2106294	0.90[MEX][hapmap]
rs2240424	0.82[JPT][hapmap]
rs2240427	0.86[JPT][hapmap]
rs2267168	0.86[JPT][hapmap]
rs2283882	0.82[JPT][hapmap]
rs2413035	0.90[MEX][hapmap]
rs2899161	0.86[JPT][hapmap]
rs4141404	0.90[MEX][hapmap]
rs4561750	0.93[LWK][hapmap];1.00[YRI][hapmap]
rs4603880	0.85[MEX][hapmap]
rs4820043	0.90[MEX][hapmap]
rs4820948	0.93[EUR][1000 genomes]
rs5749222	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5749224	0.81[AMR][1000 genomes]
rs5749225	0.86[JPT][hapmap]
rs5749229	0.90[MEX][hapmap]
rs5749232	1.00[YRI][hapmap]
rs5749236	0.86[JPT][hapmap]
rs5749240	0.86[JPT][hapmap]
rs5749252	0.86[JPT][hapmap]
rs5749255	0.86[JPT][hapmap]
rs5753485	0.86[JPT][hapmap]
rs5753486	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5753488	1.00[YRI][hapmap]
rs5753494	0.86[JPT][hapmap]
rs5753495	0.81[CHB][hapmap];0.87[JPT][hapmap]
rs5753511	0.86[JPT][hapmap]
rs5753516	0.86[JPT][hapmap]
rs5753519	0.85[JPT][hapmap]
rs5753525	0.85[JPT][hapmap]
rs5753526	0.86[JPT][hapmap]
rs5753527	0.86[JPT][hapmap]
rs5753535	0.86[JPT][hapmap]
rs5753566	0.86[JPT][hapmap]
rs5753572	0.86[JPT][hapmap]
rs5997896	0.93[EUR][1000 genomes]
rs5997897	0.93[EUR][1000 genomes]
rs5997921	0.86[JPT][hapmap]
rs5997959	0.82[JPT][hapmap]
rs6518737	0.88[CEU][hapmap];0.83[GIH][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs713619	0.86[JPT][hapmap]
rs714909	0.85[MEX][hapmap]
rs7286926	0.86[JPT][hapmap]
rs7292620	0.86[JPT][hapmap]
rs737684	0.82[CEU][hapmap]
rs737887	0.85[MEX][hapmap]
rs737888	0.90[MEX][hapmap]
rs8135417	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[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];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs874356	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs878718	1.00[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs886074	1.00[YRI][hapmap]
rs9619178	0.86[JPT][hapmap]
rs9621212	0.86[JPT][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	nsv459871	chr22:31551160-31680624	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	nsv588893	chr22:31551160-31680624	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs5997893	MN1	cis	parietal	SCAN
rs5997893	DRG1	Cis_1M	lymphoblastoid	RTeQTL
rs5997893	CRYBB1	cis	cerebellum	SCAN
rs5997893	SFI1	cis	cerebellum	SCAN
rs5997893	PISD	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31555000-31556800	Active TSS	Primary T killer memory cells from peripheral blood	blood
2	chr22:31555200-31556600	Active TSS	Fetal Brain Female	brain
3	chr22:31555400-31556200	Enhancers	Fetal Brain Male	brain
4	chr22:31555400-31556400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr22:31555400-31556400	Active TSS	Primary T cells from cord blood	blood
6	chr22:31555400-31556400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr22:31555400-31556600	Active TSS	Stomach Smooth Muscle	stomach
8	chr22:31555400-31556800	Active TSS	Primary hematopoietic stem cells short term culture	blood
9	chr22:31555400-31556800	Active TSS	Primary T helper cells PMA-I stimulated	--
10	chr22:31555400-31556800	Active TSS	Brain Angular Gyrus	brain
11	chr22:31555400-31556800	Active TSS	GM12878-XiMat	blood
12	chr22:31555400-31556800	Active TSS	K562	blood
13	chr22:31555400-31557000	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr22:31555400-31557000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr22:31555400-31557000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr22:31555400-31557000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr22:31555400-31557000	Active TSS	Liver	Liver
18	chr22:31555400-31557000	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr22:31555400-31557200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr22:31555400-31557200	Active TSS	NHEK	skin
21	chr22:31555400-31558400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr22:31555600-31556200	Active TSS	Brain Germinal Matrix	brain
23	chr22:31555600-31556400	Active TSS	Primary T helper cells fromperipheralblood	blood
24	chr22:31555600-31556400	Active TSS	Rectal Mucosa Donor 31	rectum
25	chr22:31555600-31556400	Active TSS	HepG2	liver
26	chr22:31555600-31556600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
27	chr22:31555600-31556600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
28	chr22:31555600-31556600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
29	chr22:31555600-31556600	Active TSS	Brain Anterior Caudate	brain
30	chr22:31555600-31556600	Active TSS	Fetal Thymus	thymus
31	chr22:31555600-31556600	Active TSS	Thymus	Thymus
32	chr22:31555600-31556800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr22:31555600-31556800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr22:31555600-31556800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr22:31555600-31556800	Active TSS	Brain Cingulate Gyrus	brain
36	chr22:31555600-31556800	Active TSS	Brain Hippocampus Middle	brain
37	chr22:31555600-31556800	Active TSS	Brain Inferior Temporal Lobe	brain
38	chr22:31555600-31556800	Active TSS	Brain Substantia Nigra	brain
39	chr22:31555600-31556800	Active TSS	Colon Smooth Muscle	Colon
40	chr22:31555600-31556800	Active TSS	Placenta	Placenta
41	chr22:31555600-31556800	Active TSS	Rectal Smooth Muscle	rectum
42	chr22:31555600-31556800	Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr22:31555600-31556800	Active TSS	Hela-S3	cervix
44	chr22:31555600-31556800	Active TSS	NH-A	brain
45	chr22:31555600-31556800	Active TSS	Osteobl	bone
46	chr22:31555600-31557000	Active TSS	HUES6 Cell Line	embryonic stem cell
47	chr22:31555600-31557000	Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr22:31555600-31557000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr22:31555600-31557000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr22:31555600-31557000	Active TSS	Fetal Kidney	kidney

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