Variant report

Variant	rs16988803
Chromosome Location	chr22:30987960-30987961
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:367)
CpG islands
(count:61)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:367 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr22:30987776-30988334	K562	blood:	n/a	n/a
2	TCF12	chr22:30987638-30988460	ECC-1	luminal epithelium:	n/a	n/a
3	FOXM1	chr22:30987830-30988584	ECC-1	luminal epithelium:	n/a	n/a
4	ATF2	chr22:30987737-30988332	GM12878	blood:	n/a	n/a
5	TBP	chr22:30987538-30988337	GM12878	blood:	n/a	n/a
6	SPI1	chr22:30987725-30988075	GM12891	blood:	n/a	n/a
7	SP4	chr22:30987636-30988386	H1-hESC	embryonic stem cell:	n/a	chr22:30988167-30988178
8	ZNF143	chr22:30987697-30988457	GM12878	blood:	n/a	n/a
9	ETS1	chr22:30987690-30988355	K562	blood:	n/a	n/a
10	POLR2A	chr22:30987671-30988043	HepG2	liver:	n/a	n/a
11	MTA3	chr22:30987659-30988247	GM12878	blood:	n/a	n/a
12	YY1	chr22:30987746-30988509	SK-N-SH_RA	brain:	n/a	n/a
13	NFIC	chr22:30987794-30988356	HepG2	liver:	n/a	n/a
14	ELF1	chr22:30987744-30988342	K562	blood:	n/a	chr22:30987744-30987756
15	MYC	chr22:30987108-30988538	A549	lung:	n/a	n/a
16	PAX5	chr22:30987922-30988450	GM12878	blood:	n/a	n/a
17	GTF2F1	chr22:30987780-30988311	K562	blood:	n/a	n/a
18	MAX	chr22:30987699-30988417	GM12878	blood:	n/a	n/a
19	POLR2A	chr22:30987085-30988246	H1-hESC	embryonic stem cell:	n/a	n/a
20	FOXA1	chr22:30987819-30988310	HepG2	liver:	n/a	n/a
21	SP1	chr22:30987629-30988480	A549	lung:	n/a	chr22:30987757-30987767 chr22:30988316-30988325 chr22:30988167-30988178
22	RELA	chr22:30987757-30988409	GM19099	blood:	n/a	chr22:30987977-30987986 chr22:30987977-30987986
23	PML	chr22:30987138-30988569	GM12878	blood:	n/a	n/a
24	SP1	chr22:30987761-30988423	H1-hESC	embryonic stem cell:	n/a	chr22:30988316-30988325 chr22:30988167-30988178
25	USF1	chr22:30987723-30988051	SK-N-SH_RA	brain:	n/a	chr22:30987878-30987887
26	POLR2A	chr22:30987291-30988090	MCF-7	breast:	n/a	n/a
27	POLR2A	chr22:30987594-30988081	SK-N-SH	brain:	n/a	n/a
28	USF1	chr22:30987668-30988395	SK-N-SH	brain:	n/a	chr22:30987878-30987887
29	SP1	chr22:30987748-30988497	A549	lung:	n/a	chr22:30987757-30987767 chr22:30988316-30988325 chr22:30988167-30988178
30	USF1	chr22:30987600-30988439	ECC-1	luminal epithelium:	n/a	chr22:30987878-30987887
31	SPI1	chr22:30987631-30988539	HL-60	blood:	n/a	n/a
32	MAZ	chr22:30987750-30988388	HepG2	liver:	n/a	n/a
33	CHD2	chr22:30987758-30988420	GM12878	blood:	n/a	n/a
34	SIX5	chr22:30987714-30988399	A549	lung:	n/a	n/a
35	TCF12	chr22:30987695-30988534	ECC-1	luminal epithelium:	n/a	n/a
36	ATF3	chr22:30987680-30988345	GM12878	blood:	n/a	n/a
37	CREB1	chr22:30987670-30988411	HepG2	liver:	n/a	n/a
38	TAF1	chr22:30987609-30988193	H1-hESC	embryonic stem cell:	n/a	n/a
39	FOSL2	chr22:30987750-30988371	A549	lung:	n/a	n/a
40	GABPA	chr22:30987666-30988430	MCF-7	breast:	n/a	n/a
41	MAFF	chr22:30987860-30988358	HepG2	liver:	n/a	n/a
42	EGR1	chr22:30987568-30988007	K562	blood:	n/a	chr22:30987741-30987763 chr22:30987746-30987759 chr22:30987747-30987758 chr22:30987746-30987756 chr22:30987746-30987759 chr22:30987747-30987756 chr22:30987746-30987759 chr22:30987746-30987759 chr22:30987747-30987757 chr22:30987745-30987759 chr22:30987747-30987757 chr22:30987745-30987760
43	SPI1	chr22:30987723-30987966	HL-60	blood:	n/a	n/a
44	USF1	chr22:30987716-30988030	HepG2	liver:	n/a	chr22:30987878-30987887
45	ELF1	chr22:30987766-30988482	A549	lung:	n/a	n/a
46	SPI1	chr22:30987737-30987987	K562	blood:	n/a	n/a
47	SPI1	chr22:30987749-30987994	K562	blood:	n/a	n/a
48	POLR2A	chr22:30987192-30988052	Hela-S3	cervix:	n/a	n/a
49	MAZ	chr22:30986755-30988532	IMR90	lung:	n/a	n/a
50	CEBPB	chr22:30987737-30988287	HepG2	liver:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr22:30987935-30987985	AG09309	skin:	n/a
2	chr22:30987935-30987985	HRPEpiC	eye:	n/a
3	chr22:30987935-30987985	Hela-S3	cervix:	n/a
4	chr22:30987935-30987985	K562	blood:	n/a
5	chr22:30987935-30987985	GM12878	blood:	n/a
6	chr22:30987935-30987985	HL-60	blood:	n/a
7	chr22:30987935-30987985	HAEpiC	amniotic membrane:	n/a
8	chr22:30987935-30987985	HRCEpiC	kidney:	n/a
9	chr22:30987935-30987985	HUVEC	blood vessel:	n/a
10	chr22:30987935-30987985	HEEpiC	esophagus:	n/a
11	chr22:30987935-30987985	GM12891	blood:	n/a
12	chr22:30987935-30987985	SK-N-SH_RA	brain:	n/a
13	chr22:30987935-30987985	SKMC	muscle:	n/a
14	chr22:30987935-30987985	HNPCEpiC	eye:	n/a
15	chr22:30987935-30987985	ECC-1	luminal epithelium:	n/a
16	chr22:30987935-30987985	T-47D	breast:	n/a
17	chr22:30987935-30987985	MCF10A-Er-Src	breast:	n/a
18	chr22:30987935-30987985	Caco-2	colon:	n/a
19	chr22:30987935-30987985	NB4	blood:	n/a
20	chr22:30987935-30987985	LNCaP	prostate:	n/a
21	chr22:30987935-30987985	PFSK-1	brain:	n/a
22	chr22:30987935-30987985	PANC-1	pancreas:	n/a
23	chr22:30987935-30987985	NHBE	bronchial:	n/a
24	chr22:30987935-30987985	SK-N-MC	brain:	n/a
25	chr22:30987935-30987985	GM19239	blood:	n/a
26	chr22:30987935-30987985	MCF-7	breast:	n/a
27	chr22:30987935-30987985	HIPEpiC	eye:	n/a
28	chr22:30987935-30987985	HMEC	breast:	n/a
29	chr22:30987935-30987985	HCM	heart:	n/a
30	chr22:30987935-30987985	Jurkat	blood:	n/a
31	chr22:30987935-30987985	CMK	blood:	n/a
32	chr22:30987935-30987985	GM12892	blood:	n/a
33	chr22:30987935-30987985	AoSMC	blood vessel:	n/a
34	chr22:30987935-30987985	HRE	kidney:	n/a
35	chr22:30987935-30987985	SK-N-SH	brain:	n/a
36	chr22:30987935-30987985	HEK293	kidney:	embryo
37	chr22:30987935-30987985	NHDF-neo	bronchial:	n/a
38	chr22:30987935-30987985	H1-hESC	embryonic stem cell:	embryo
39	chr22:30987935-30987985	NH-A	brain:	n/a
40	chr22:30987935-30987985	IMR90	lung:	fetal
41	chr22:30987935-30987985	AG10803	skin:	n/a
42	chr22:30987935-30987985	Hepatocyte	liver:	n/a
43	chr22:30987935-30987985	BJ	skin:	n/a
44	chr22:30987935-30987985	HepG2	liver:	n/a
45	chr22:30987935-30987985	A549	lung:	n/a
46	chr22:30987935-30987985	NT2-D1	testis:	n/a
47	chr22:30987935-30987985	AG04450	lung:	fetal
48	chr22:30987935-30987985	PrEC	prostate:	n/a
49	chr22:30987935-30987985	SAEC	small airway:	n/a
50	chr22:30987935-30987985	AG09319	gingival:	n/a

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:30987737..30989936-chr22:31002004..31003702,2	MCF-7	breast:
2	chr22:30983113..30985414-chr22:30986213..30988243,5	MCF-7	breast:
3	chr22:30987634..30988149-chr4:57253320..57254113,2	MCF-7	breast:
4	chr22:30968228..30973884-chr22:30985019..30988219,5	MCF-7	breast:
5	chr22:30969461..30973158-chr22:30985013..30988022,5	MCF-7	breast:

No data

Variant related genes	Relation type
PES1	TF binding region
PES1	CpG island
ENSG00000128242	Chromatin interaction
ENSG00000100029	Chromatin interaction
ENSG00000185339	Chromatin interaction
ENSG00000157426	Chromatin interaction
ENSG00000269921	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1008801	1.00[JPT][hapmap]
rs11912540	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs11913206	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11913547	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11914005	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11914168	0.90[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12484495	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12484688	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13750	1.00[JPT][hapmap]
rs16988810	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16988814	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17526668	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17670808	1.00[JPT][hapmap]
rs17738527	1.00[JPT][hapmap]
rs17738540	1.00[JPT][hapmap]
rs34236034	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820019	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820869	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.98[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820873	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820874	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820877	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6518693	1.00[JPT][hapmap]
rs7289820	1.00[JPT][hapmap]
rs73881484	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73881485	1.00[ASN][1000 genomes]
rs73881486	1.00[ASN][1000 genomes]
rs8138759	1.00[JPT][hapmap]
rs8141286	1.00[JPT][hapmap]
rs9606735	1.00[JPT][hapmap]
rs9606736	1.00[JPT][hapmap]
rs9606738	1.00[JPT][hapmap]
rs9606739	1.00[JPT][hapmap]
rs9608938	1.00[JPT][hapmap]
rs9608941	1.00[JPT][hapmap]
rs9608942	1.00[JPT][hapmap]
rs9608944	1.00[JPT][hapmap]
rs9608956	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
3	nsv588887	chr22:30953521-30995356	Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv834175	chr22:30976624-31089545	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs16988803	SLC35E4	cis	cerebellum	SCAN
rs16988803	TCN2	cis	parietal	SCAN
rs16988803	MTMR3	cis	cerebellum	SCAN
rs16988803	C22orf27	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30986200-30988200	Active TSS	H9 Cell Line	embryonic stem cell
2	chr22:30986400-30988600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr22:30986600-30988200	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr22:30986600-30988200	Active TSS	H1 Cell Line	embryonic stem cell
5	chr22:30986600-30988200	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr22:30986600-30988600	Active TSS	Fetal Kidney	kidney
7	chr22:30986800-30988000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr22:30986800-30988200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr22:30986800-30988200	Active TSS	Fetal Muscle Trunk	muscle
10	chr22:30986800-30988200	Active TSS	K562	blood
11	chr22:30986800-30988400	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr22:30986800-30988600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr22:30986800-30988600	Active TSS	Psoas Muscle	Psoas
14	chr22:30986800-30988600	Active TSS	A549	lung
15	chr22:30987000-30988000	Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr22:30987000-30988000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr22:30987000-30988000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr22:30987000-30988000	Flanking Active TSS	Primary hematopoietic stem cells	blood
19	chr22:30987000-30988000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
20	chr22:30987000-30988000	Active TSS	Lung	lung
21	chr22:30987000-30988000	Active TSS	Small Intestine	intestine
22	chr22:30987000-30988200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr22:30987000-30988200	Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr22:30987000-30988200	Active TSS	GM12878-XiMat	blood
25	chr22:30987000-30988400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr22:30987000-30988400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr22:30987000-30988400	Active TSS	Left Ventricle	heart
28	chr22:30987000-30988600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr22:30987000-30988600	Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr22:30987000-30988600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr22:30987000-30988600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr22:30987000-30988600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr22:30987000-30988600	Active TSS	HSMM	muscle
34	chr22:30987000-30988600	Active TSS	NHDF-Ad	bronchial
35	chr22:30987000-30988600	Active TSS	NHEK	skin
36	chr22:30987200-30988000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr22:30987200-30988000	Active TSS	Placenta Amnion	Placenta Amnion
38	chr22:30987200-30988000	Active TSS	Spleen	Spleen
39	chr22:30987200-30988200	Active TSS	HUES64 Cell Line	embryonic stem cell
40	chr22:30987200-30988200	Active TSS	Aorta	Aorta
41	chr22:30987200-30988200	Active TSS	Fetal Intestine Small	intestine
42	chr22:30987200-30988200	Active TSS	Gastric	stomach
43	chr22:30987200-30988200	Active TSS	HMEC	breast
44	chr22:30987200-30988400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr22:30987200-30988400	Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr22:30987200-30988400	Active TSS	Muscle Satellite Cultured Cells	--
47	chr22:30987200-30988400	Active TSS	Fetal Stomach	stomach
48	chr22:30987200-30988400	Active TSS	Hela-S3	cervix
49	chr22:30987200-30988400	Active TSS	NHLF	lung
50	chr22:30987200-30988400	Active TSS	Osteobl	bone

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