Variant report

Variant	rs16931988
Chromosome Location	chr9:116038508-116038509
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:56)
CpG islands
(count:0)
Chromatin interactive
region (count:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:56 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:116036438-116039178	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr9:116037426-116038757	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr9:116037351-116038891	HepG2	liver:	n/a	n/a
4	POLR2A	chr9:116036883-116039038	H1-hESC	embryonic stem cell:	n/a	n/a
5	SIN3AK20	chr9:116036628-116038581	MCF-7	breast:	n/a	n/a
6	RELA	chr9:116037479-116038514	GM10847	blood:	n/a	n/a
7	SPI1	chr9:116037513-116038730	GM12878	blood:	n/a	chr9:116038135-116038148 chr9:116038312-116038325
8	POLR2A	chr9:116036665-116039023	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr9:116036286-116038980	GM12891	blood:	n/a	n/a
10	POLR2A	chr9:116036757-116038891	GM18505	blood:	n/a	n/a
11	MYC	chr9:116038432-116038772	MCF10A-Er-Src	breast:	n/a	n/a
12	CHD1	chr9:116035600-116039131	IMR90	lung:	n/a	n/a
13	POLR2A	chr9:116037343-116038892	Raji	blood:	n/a	n/a
14	POLR2A	chr9:116037507-116038577	GM12892	blood:	n/a	n/a
15	CEBPB	chr9:116037709-116038585	Hela-S3	cervix:	n/a	n/a
16	TBP	chr9:116036601-116038597	Hela-S3	cervix:	n/a	n/a
17	RAD21	chr9:116036238-116039041	SK-N-SH	brain:	n/a	chr9:116037583-116037595 chr9:116038010-116038023
18	MYC	chr9:116036669-116038515	K562	blood:	n/a	chr9:116037899-116037908
19	POLR2A	chr9:116037232-116039041	SK-N-MC	brain:	n/a	n/a
20	GABPA	chr9:116037238-116038608	A549	lung:	n/a	n/a
21	SIN3A	chr9:116036705-116038652	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr9:116036665-116038914	K562	blood:	n/a	n/a
23	HEY1	chr9:116037324-116038510	K562	blood:	n/a	chr9:116037870-116037885
24	SIX5	chr9:116037377-116038689	A549	lung:	n/a	n/a
25	POLR2A	chr9:116037465-116038770	K562	blood:	n/a	n/a
26	SIN3AK20	chr9:116037740-116038544	A549	lung:	n/a	n/a
27	MXI1	chr9:116037374-116038597	Hela-S3	cervix:	n/a	chr9:116037526-116037541 chr9:116037528-116037543
28	CBX3	chr9:116037549-116038508	K562	blood:	n/a	n/a
29	POLR2A	chr9:116037324-116038508	GM12878	blood:	n/a	n/a
30	POLR2A	chr9:116036745-116038941	K562	blood:	n/a	n/a
31	GABPA	chr9:116037029-116038797	MCF-7	breast:	n/a	n/a
32	POLR2A	chr9:116036808-116039003	GM12878	blood:	n/a	n/a
33	GABPA	chr9:116037249-116038654	A549	lung:	n/a	n/a
34	MXI1	chr9:116036564-116038986	SK-N-SH	brain:	n/a	chr9:116037526-116037541 chr9:116037528-116037543
35	MXI1	chr9:116036771-116038702	GM12878	blood:	n/a	chr9:116037526-116037541 chr9:116037528-116037543
36	MXI1	chr9:116036932-116038664	IMR90	lung:	n/a	chr9:116037526-116037541 chr9:116037528-116037543
37	POLR2A	chr9:116037368-116038959	K562	blood:	n/a	n/a
38	CTCF	chr9:116035968-116038774	SK-N-SH	brain:	n/a	n/a
39	POLR2A	chr9:116036819-116038979	HepG2	liver:	n/a	n/a
40	REST	chr9:116036615-116038610	H1-neurons	neurons:	n/a	n/a
41	POLR2A	chr9:116037414-116038670	GM12878	blood:	n/a	n/a
42	ATF2	chr9:116037518-116038613	GM12878	blood:	n/a	n/a
43	IRF3	chr9:116038426-116038838	GM12878	blood:	n/a	n/a
44	MAX	chr9:116037688-116038637	A549	lung:	n/a	chr9:116037899-116037908
45	POLR2A	chr9:116036332-116039038	IMR90	lung:	n/a	n/a
46	POLR2A	chr9:116037276-116038804	Hela-S3	cervix:	n/a	n/a
47	SPI1	chr9:116038215-116038571	HL-60	blood:	n/a	chr9:116038312-116038325
48	SMC3	chr9:116037345-116038708	Hela-S3	cervix:	n/a	n/a
49	TBP	chr9:116036663-116038578	K562	blood:	n/a	n/a
50	HCFC1	chr9:116036232-116038897	Hela-S3	cervix:	n/a	n/a

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:116037849..116040056-chr9:116062437..116065582,3	MCF-7	breast:
2	chr9:116036437..116039850-chr9:116170281..116174782,6	K562	blood:
3	chr9:115981728..115986983-chr9:116035777..116040437,9	K562	blood:
4	chr9:116035556..116040148-chr9:116171147..116174619,7	K562	blood:
5	chr9:116038235..116040898-chr9:116423469..116425169,2	MCF-7	breast:
6	chr9:115512698..115514461-chr9:116038293..116041061,2	MCF-7	breast:
7	chr9:116036612..116039217-chr9:116063138..116067985,4	MCF-7	breast:
8	chr9:116036323..116039598-chr9:116161482..116165034,3	MCF-7	breast:
9	chr9:116033413..116040476-chr9:116169994..116174441,15	MCF-7	breast:
10	chr9:116036740..116039923-chr9:116057646..116061284,5	MCF-7	breast:
11	chr9:116037889..116039423-chr9:116171987..116174165,2	MCF-7	breast:
12	chr9:116036224..116039468-chr9:116162090..116165920,4	MCF-7	breast:
13	chr9:116038438..116040494-chr9:116158946..116160891,2	MCF-7	breast:
14	chr16:18812479..18813318-chr9:116037697..116038544,2	Hela-S3	cervix:
15	chr9:115982005..115986983-chr9:116035777..116039702,5	K562	blood:
16	chr9:116036349..116038748-chr9:116343941..116345814,2	K562	blood:
17	chr9:116037991..116040071-chr9:116101087..116104221,4	MCF-7	breast:
18	chr9:116035986..116039204-chr9:116098421..116104240,5	MCF-7	breast:
19	chr9:115983488..115985496-chr9:116035418..116038927,3	MCF-7	breast:
20	chr9:116038056..116040048-chr9:116108621..116111534,2	MCF-7	breast:

No data

Variant related genes	Relation type
PRPF4	TF binding region
CDC26	TF binding region
ENSG00000148218	Chromatin interaction
ENSG00000165188	Chromatin interaction
ENSG00000226609	Chromatin interaction
ENSG00000148158	Chromatin interaction
ENSG00000260342	Chromatin interaction
ENSG00000170540	Chromatin interaction
ENSG00000148225	Chromatin interaction
ENSG00000148229	Chromatin interaction
ENSG00000138835	Chromatin interaction
ENSG00000119321	Chromatin interaction
ENSG00000157653	Chromatin interaction
ENSG00000136868	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10117320	1.00[EUR][1000 genomes]
rs10123780	0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs10125032	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12337200	1.00[EUR][1000 genomes]
rs12337498	0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs12337709	0.88[AFR][1000 genomes]
rs12342489	1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs3087548	0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs3810917	0.96[YRI][hapmap]
rs3810918	0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs73552275	1.00[EUR][1000 genomes]
rs7858004	1.00[EUR][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	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv1042663	chr9:115920158-116167140	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv893744	chr9:115934852-116170227	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116036600-116038600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr9:116036600-116038600	Active TSS	K562	blood
3	chr9:116036600-116038800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr9:116036800-116038600	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr9:116036800-116038600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr9:116036800-116038600	Active TSS	H9 Cell Line	embryonic stem cell
7	chr9:116036800-116038600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:116036800-116038600	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr9:116036800-116038600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr9:116036800-116038600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr9:116036800-116038600	Active TSS	Muscle Satellite Cultured Cells	--
12	chr9:116036800-116038600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr9:116036800-116038600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr9:116036800-116038600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr9:116036800-116038600	Active TSS	Aorta	Aorta
16	chr9:116036800-116038600	Active TSS	Fetal Intestine Large	intestine
17	chr9:116036800-116038600	Active TSS	Fetal Intestine Small	intestine
18	chr9:116036800-116038600	Active TSS	Fetal Stomach	stomach
19	chr9:116036800-116038600	Active TSS	Fetal Thymus	thymus
20	chr9:116036800-116038600	Active TSS	Placenta Amnion	Placenta Amnion
21	chr9:116036800-116038600	Active TSS	Psoas Muscle	Psoas
22	chr9:116036800-116038600	Active TSS	GM12878-XiMat	blood
23	chr9:116036800-116038600	Active TSS	NHDF-Ad	bronchial
24	chr9:116036800-116038600	Active TSS	NHEK	skin
25	chr9:116036800-116038800	Active TSS	H1 Cell Line	embryonic stem cell
26	chr9:116036800-116038800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr9:116036800-116038800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr9:116036800-116038800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr9:116036800-116038800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
30	chr9:116036800-116038800	Active TSS	Fetal Muscle Trunk	muscle
31	chr9:116036800-116038800	Active TSS	A549	lung
32	chr9:116036800-116039000	Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr9:116036800-116039000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr9:116036800-116039000	Active TSS	HSMM	muscle
35	chr9:116036800-116039200	Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr9:116036800-116039200	Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr9:116037000-116038600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr9:116037000-116038600	Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr9:116037000-116038600	Active TSS	Placenta	Placenta
40	chr9:116037000-116038600	Active TSS	Lung	lung
41	chr9:116037000-116038600	Active TSS	Pancreas	Pancrea
42	chr9:116037000-116038600	Active TSS	Sigmoid Colon	Sigmoid Colon
43	chr9:116037000-116038600	Active TSS	Small Intestine	intestine
44	chr9:116037000-116038800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr9:116037000-116038800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr9:116037000-116038800	Active TSS	Left Ventricle	heart
47	chr9:116037000-116038800	Bivalent/Poised TSS	HepG2	liver
48	chr9:116037000-116039000	Active TSS	Esophagus	oesophagus
49	chr9:116037000-116039000	Active TSS	Ovary	ovary
50	chr9:116037200-116038600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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