Variant report

Variant	rs28452481
Chromosome Location	chr9:137030545-137030546
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	TBP	chr9:137029490-137030595	H1-hESC	embryonic stem cell:	n/a	chr9:137029709-137029720
2	POLR2A	chr9:137029538-137030882	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr9:137029999-137030888	MCF-7	breast:	n/a	n/a
4	GTF3C2	chr9:137028928-137030946	Hela-S3	cervix:	n/a	n/a
5	HEY1	chr9:137029439-137030683	HepG2	liver:	n/a	n/a
6	MYC	chr9:137030456-137030795	MCF-7	breast:	n/a	chr9:137030658-137030668
7	EP300	chr9:137029373-137030814	A549	lung:	n/a	chr9:137030168-137030177 chr9:137030107-137030114 chr9:137030185-137030194
8	MYC	chr9:137029628-137030953	MCF10A-Er-Src	breast:	n/a	chr9:137030658-137030668
9	PAX5	chr9:137029945-137030631	GM12892	blood:	n/a	chr9:137029986-137029995 chr9:137030050-137030059
10	E2F6	chr9:137029868-137030847	K562	blood:	n/a	chr9:137030185-137030194 chr9:137030548-137030557 chr9:137030176-137030185 chr9:137030029-137030040 chr9:137030028-137030040
11	E2F4	chr9:137029539-137030547	MCF10A-Er-Src	breast:	n/a	chr9:137030185-137030194 chr9:137030176-137030185 chr9:137030028-137030040 chr9:137030029-137030040
12	GTF3C2	chr9:137029942-137030788	K562	blood:	n/a	n/a
13	POLR2A	chr9:137029904-137030611	HepG2	liver:	n/a	n/a
14	FOXA1	chr9:137030511-137030889	T-47D	breast:	n/a	chr9:137030629-137030644
15	ELF1	chr9:137029682-137030745	GM12878	blood:	n/a	chr9:137030187-137030199 chr9:137030105-137030118
16	POLR2A	chr9:137029526-137030898	H1-neurons	neurons:	n/a	n/a
17	CHD2	chr9:137029513-137030734	Hela-S3	cervix:	n/a	n/a
18	FOXA1	chr9:137030463-137030814	T-47D	breast:	n/a	chr9:137030629-137030644
19	MAX	chr9:137029557-137030872	H1-hESC	embryonic stem cell:	n/a	chr9:137030658-137030668
20	SETDB1	chr9:137028976-137030885	U2OS	brain:	n/a	chr9:137030176-137030185
21	MYC	chr9:137029559-137031082	NB4	blood:	n/a	chr9:137030658-137030668
22	KAP1	chr9:137029034-137030794	U2OS	brain:	n/a	n/a
23	BCL3	chr9:137029450-137030936	A549	lung:	n/a	chr9:137030050-137030059
24	TCF7L2	chr9:137029568-137030813	HCT-116	colon:	n/a	n/a
25	POLR2A	chr9:137028481-137030843	GM18505	blood:	n/a	n/a
26	CEBPB	chr9:137029855-137030786	MCF-7	breast:	n/a	n/a
27	POU2F2	chr9:137029418-137030784	GM12891	blood:	n/a	n/a
28	POLR2A	chr9:137030410-137030798	GM12891	blood:	n/a	n/a
29	TAF1	chr9:137029892-137030566	GM12878	blood:	n/a	n/a
30	TBL1XR1	chr9:137029536-137030770	K562	blood:	n/a	n/a
31	SIN3A	chr9:137029631-137030708	GM12878	blood:	n/a	chr9:137030119-137030132
32	HCFC1	chr9:137029561-137030755	K562	blood:	n/a	n/a
33	ZNF143	chr9:137029589-137030622	GM12878	blood:	n/a	chr9:137030184-137030194
34	POLR2A	chr9:137030086-137030723	ProgFib	skin:	n/a	n/a
35	GABPA	chr9:137029424-137030824	SK-N-SH	brain:	n/a	chr9:137030172-137030186 chr9:137030175-137030189 chr9:137030168-137030177 chr9:137030175-137030184 chr9:137030183-137030197 chr9:137030547-137030558 chr9:137030177-137030186 chr9:137030175-137030186
36	CTCF	chr9:137030528-137030699	GM12892	blood:	n/a	n/a
37	MYC	chr9:137029803-137030823	H1-hESC	embryonic stem cell:	n/a	chr9:137030658-137030668
38	SIN3A	chr9:137029602-137030770	H1-hESC	embryonic stem cell:	n/a	chr9:137030119-137030132
39	POLR2A	chr9:137030433-137030775	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr9:137029956-137030777	GM12892	blood:	n/a	n/a
41	FOXP2	chr9:137029852-137030810	PFSK-1	brain:	n/a	n/a
42	MYC	chr9:137030401-137030698	HUVEC	blood vessel:	n/a	chr9:137030658-137030668
43	POLR2A	chr9:137028437-137030891	GM19099	blood:	n/a	n/a
44	TEAD4	chr9:137029335-137030697	SK-N-SH	brain:	n/a	n/a
45	FOSL2	chr9:137029335-137030775	A549	lung:	n/a	n/a
46	IRF1	chr9:137029500-137030810	K562	blood:	n/a	n/a
47	MAX	chr9:137028694-137030859	Hela-S3	cervix:	n/a	chr9:137030658-137030668
48	MYBL2	chr9:137029353-137030596	HepG2	liver:	n/a	n/a
49	E2F1	chr9:137029863-137030793	Hela-S3	cervix:	n/a	chr9:137030185-137030194 chr9:137030548-137030557 chr9:137030176-137030185 chr9:137030028-137030040
50	POLR2A	chr9:137029530-137031078	K562	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr9:137030544-137030594	HUVEC	blood vessel:	n/a
2	chr9:137030544-137030594	K562	blood:	n/a
3	chr9:137030544-137030594	GM06990	blood:	n/a
4	chr9:137030544-137030594	NT2-D1	testis:	n/a
5	chr9:137030544-137030594	NHDF-neo	bronchial:	n/a
6	chr9:137030544-137030594	HNPCEpiC	eye:	n/a
7	chr9:137030544-137030594	HCT-116	colon:	n/a
8	chr9:137030544-137030594	SK-N-MC	brain:	n/a
9	chr9:137030544-137030594	MCF-7	breast:	n/a
10	chr9:137030544-137030594	BE2_C	brain:	n/a
11	chr9:137030544-137030594	NHBE	bronchial:	n/a
12	chr9:137030544-137030594	CMK	blood:	n/a
13	chr9:137030544-137030594	GM19239	blood:	n/a
14	chr9:137030544-137030594	SKMC	muscle:	n/a
15	chr9:137030544-137030594	PrEC	prostate:	n/a
16	chr9:137030544-137030594	Jurkat	blood:	n/a
17	chr9:137030544-137030594	HRCEpiC	kidney:	n/a
18	chr9:137030544-137030594	HL-60	blood:	n/a
19	chr9:137030544-137030594	A549	lung:	n/a
20	chr9:137030544-137030594	HPAEpiC	pulmonary alveolar:	n/a
21	chr9:137030544-137030594	SK-N-SH	brain:	n/a
22	chr9:137030544-137030594	H1-hESC	embryonic stem cell:	embryo
23	chr9:137030544-137030594	AG04450	lung:	fetal
24	chr9:137030544-137030594	GM12891	blood:	n/a
25	chr9:137030544-137030594	HIPEpiC	eye:	n/a
26	chr9:137030544-137030594	HRPEpiC	eye:	n/a
27	chr9:137030544-137030594	RPTEC	kidney:	n/a
28	chr9:137030544-137030594	SAEC	small airway:	n/a
29	chr9:137030544-137030594	AG04449	skin:	fetal
30	chr9:137030544-137030594	NH-A	brain:	n/a
31	chr9:137030544-137030594	ovcar-3	ovarian:	n/a
32	chr9:137030544-137030594	Hepatocyte	liver:	n/a
33	chr9:137030544-137030594	SK-N-SH_RA	brain:	n/a
34	chr9:137030544-137030594	U87	brain:	n/a
35	chr9:137030544-137030594	BJ	skin:	n/a
36	chr9:137030544-137030594	AoSMC	blood vessel:	n/a
37	chr9:137030544-137030594	HepG2	liver:	n/a
38	chr9:137030544-137030594	AG09309	skin:	n/a
39	chr9:137030544-137030594	PANC-1	pancreas:	n/a
40	chr9:137030544-137030594	GM12878	blood:	n/a
41	chr9:137030544-137030594	LNCaP	prostate:	n/a
42	chr9:137030544-137030594	MCF10A-Er-Src	breast:	n/a
43	chr9:137030544-137030594	HAEpiC	amniotic membrane:	n/a
44	chr9:137030544-137030594	ECC-1	luminal epithelium:	n/a
45	chr9:137030544-137030594	HCM	heart:	n/a
46	chr9:137030544-137030594	AG09319	gingival:	n/a
47	chr9:137030544-137030594	T-47D	breast:	n/a
48	chr9:137030544-137030594	PFSK-1	brain:	n/a
49	chr9:137030544-137030594	HCPEpiC	choroid plexus:	n/a
50	chr9:137030544-137030594	Hela-S3	cervix:	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:137030110..137032230-chr9:137037095..137040393,3	MCF-7	breast:
2	chr9:136999027..137003702-chr9:137026566..137032835,8	MCF-7	breast:
3	chr9:137028457..137030780-chr9:137033087..137036645,3	MCF-7	breast:
4	chr9:136999035..137002778-chr9:137027888..137031331,5	K562	blood:
5	chr9:137030448..137032134-chr9:137229011..137230599,2	K562	blood:
6	chr9:137029897..137032228-chr9:137170817..137173611,2	MCF-7	breast:
7	chr9:137028543..137032380-chr9:137216254..137220347,4	K562	blood:
8	chr9:137028191..137030569-chr9:137216306..137218797,3	MCF-7	breast:
9	chr9:137030267..137032802-chr9:137338931..137341494,3	MCF-7	breast:
10	chr9:137028423..137041755-chr9:137210581..137221866,35	MCF-7	breast:
11	chr9:136997943..137000936-chr9:137029556..137031957,3	K562	blood:
12	chr9:137028231..137030926-chr9:137032684..137034391,3	K562	blood:
13	chr9:137001200..137002778-chr9:137029831..137031732,3	K562	blood:

Variant related genes	Relation type
RNU6ATAC	TF binding region
ENSG00000273473	TF binding region
ENSG00000273473	CpG island
RNU6ATAC	CpG island
ENSG00000186350	Chromatin interaction
ENSG00000273249	Chromatin interaction
ENSG00000273473	Chromatin interaction
ENSG00000196363	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs28360858	1.00[EUR][1000 genomes]
rs28377785	1.00[AFR][1000 genomes]
rs28399690	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28401385	1.00[EUR][1000 genomes]
rs28412245	1.00[EUR][1000 genomes]
rs28421319	1.00[AFR][1000 genomes]
rs28425680	1.00[AFR][1000 genomes]
rs28436125	1.00[AFR][1000 genomes]
rs28440102	1.00[EUR][1000 genomes]
rs28473171	1.00[EUR][1000 genomes]
rs28479377	1.00[EUR][1000 genomes]
rs28491791	1.00[EUR][1000 genomes]
rs28507057	1.00[EUR][1000 genomes]
rs28562287	1.00[AFR][1000 genomes]
rs28562957	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28579703	1.00[EUR][1000 genomes]
rs28594106	1.00[AFR][1000 genomes]
rs28620240	1.00[EUR][1000 genomes]
rs28626085	1.00[AFR][1000 genomes]
rs28687115	1.00[AFR][1000 genomes]
rs28705689	1.00[EUR][1000 genomes]
rs28708401	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28710163	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28712382	1.00[GIH][hapmap];1.00[EUR][1000 genomes]
rs28714237	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28740804	1.00[EUR][1000 genomes]
rs28758854	1.00[GIH][hapmap];1.00[EUR][1000 genomes]
rs28759311	1.00[EUR][1000 genomes]
rs34022301	1.00[AFR][1000 genomes]
rs34079254	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34194763	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34473303	1.00[EUR][1000 genomes]
rs34546899	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34607253	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34646496	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34861636	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34929179	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35209649	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35322411	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35370793	1.00[AFR][1000 genomes]
rs35387289	1.00[EUR][1000 genomes]
rs35419030	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35448798	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35487246	0.84[EUR][1000 genomes]
rs35489314	1.00[EUR][1000 genomes]
rs35504753	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35511305	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35709000	1.00[EUR][1000 genomes]
rs35726748	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35874066	1.00[AFR][1000 genomes]
rs35924689	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35962164	1.00[AFR][1000 genomes]
rs36029182	1.00[AFR][1000 genomes]
rs71483222	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71505283	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71505284	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894138	chr9:136839840-137093168	Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription 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	34 gene(s)	inside rSNPs	diseases
2	nsv1048571	chr9:136872166-137265444	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv894148	chr9:136874066-137093168	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv894151	chr9:136887757-137397609	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	nsv894155	chr9:136969689-137364866	Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
6	esv1793302	chr9:136990615-137390602	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 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	chr9:137028000-137030600	Active TSS	H1 Cell Line	embryonic stem cell
2	chr9:137028000-137031200	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr9:137028200-137030600	Active TSS	H9 Cell Line	embryonic stem cell
4	chr9:137028200-137030600	Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr9:137028200-137030600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr9:137028200-137030600	Active TSS	Brain Angular Gyrus	brain
7	chr9:137028200-137030600	Active TSS	Brain Hippocampus Middle	brain
8	chr9:137028200-137030600	Active TSS	Colon Smooth Muscle	Colon
9	chr9:137028200-137031000	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr9:137028200-137031000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr9:137028200-137031000	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr9:137028200-137031000	Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr9:137028200-137031000	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr9:137028200-137031200	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr9:137028400-137030600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr9:137028400-137030600	Active TSS	Primary T killer memory cells from peripheral blood	blood
17	chr9:137028400-137030600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr9:137028400-137030600	Active TSS	Fetal Kidney	kidney
19	chr9:137028400-137030600	Active TSS	Psoas Muscle	Psoas
20	chr9:137028400-137030600	Active TSS	NHLF	lung
21	chr9:137028400-137031000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr9:137028600-137030600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr9:137028600-137030600	Active TSS	Primary T helper naive cells from peripheral blood	blood
24	chr9:137028600-137030600	Active TSS	Brain Substantia Nigra	brain
25	chr9:137028600-137030600	Active TSS	Ovary	ovary
26	chr9:137028600-137030600	Active TSS	Rectal Smooth Muscle	rectum
27	chr9:137028600-137030600	Active TSS	HSMM	muscle
28	chr9:137028600-137031000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr9:137028600-137031000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
30	chr9:137028600-137031000	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr9:137028800-137030600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
32	chr9:137028800-137030600	Active TSS	Brain Germinal Matrix	brain
33	chr9:137028800-137030600	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr9:137028800-137030600	Active TSS	Stomach Mucosa	stomach
35	chr9:137028800-137030600	Active TSS	HSMMtube	muscle
36	chr9:137028800-137030600	Active TSS	NHEK	skin
37	chr9:137029000-137030600	Active TSS	A549	lung
38	chr9:137029200-137030600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr9:137029600-137030800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
40	chr9:137029800-137030600	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
41	chr9:137030200-137030600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr9:137030200-137030600	Flanking Active TSS	Primary hematopoietic stem cells	blood
43	chr9:137030200-137030600	Active TSS	Aorta	Aorta
44	chr9:137030200-137030600	Active TSS	Sigmoid Colon	Sigmoid Colon
45	chr9:137030200-137030600	Active TSS	Small Intestine	intestine
46	chr9:137030200-137030800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
47	chr9:137030200-137030800	Flanking Active TSS	Primary B cells from cord blood	blood
48	chr9:137030200-137030800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
49	chr9:137030200-137030800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr9:137030200-137030800	Flanking Active TSS	Adipose Nuclei	Adipose

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