Variant report

Variant	rs28681533
Chromosome Location	chr9:137030156-137030157
allele	G/T
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	ELK1	chr9:137029552-137030409	K562	blood:	n/a	n/a
5	GTF3C2	chr9:137028928-137030946	Hela-S3	cervix:	n/a	n/a
6	ZBTB33	chr9:137029503-137030257	A549	lung:	n/a	n/a
7	POLR2A	chr9:137029384-137030485	HCT-116	colon:	n/a	n/a
8	SP1	chr9:137029504-137030259	H1-hESC	embryonic stem cell:	n/a	chr9:137029904-137029925 chr9:137030024-137030038
9	GABPA	chr9:137029656-137030339	H1-hESC	embryonic stem cell:	n/a	chr9:137030172-137030186 chr9:137030175-137030189 chr9:137030168-137030177 chr9:137030175-137030184 chr9:137030183-137030197 chr9:137030177-137030186 chr9:137030175-137030186
10	HEY1	chr9:137029439-137030683	HepG2	liver:	n/a	n/a
11	SRF	chr9:137029829-137030305	K562	blood:	n/a	n/a
12	TEAD4	chr9:137029435-137030307	ECC-1	luminal epithelium:	n/a	n/a
13	FOSL2	chr9:137029360-137030320	SK-N-SH	brain:	n/a	n/a
14	SP1	chr9:137029507-137030297	GM12878	blood:	n/a	chr9:137029904-137029925 chr9:137030024-137030038
15	CEBPB	chr9:137029607-137030510	ECC-1	luminal epithelium:	n/a	n/a
16	EP300	chr9:137029373-137030814	A549	lung:	n/a	chr9:137030168-137030177 chr9:137030107-137030114 chr9:137030185-137030194
17	ZNF143	chr9:137029602-137030411	H1-hESC	embryonic stem cell:	n/a	chr9:137030184-137030194
18	TEAD4	chr9:137029414-137030220	SK-N-SH	brain:	n/a	n/a
19	NRF1	chr9:137029621-137030388	K562	blood:	n/a	chr9:137030172-137030186 chr9:137030175-137030189 chr9:137030168-137030177 chr9:137030185-137030196 chr9:137030175-137030184 chr9:137030205-137030216 chr9:137030174-137030185 chr9:137030183-137030197 chr9:137030177-137030186 chr9:137030175-137030186
20	TCF7L2	chr9:137028865-137030362	Hela-S3	cervix:	n/a	n/a
21	MYC	chr9:137029628-137030953	MCF10A-Er-Src	breast:	n/a	chr9:137030658-137030668
22	PAX5	chr9:137029945-137030631	GM12892	blood:	n/a	chr9:137029986-137029995 chr9:137030050-137030059
23	E2F6	chr9:137029868-137030847	K562	blood:	n/a	chr9:137030185-137030194 chr9:137030548-137030557 chr9:137030176-137030185 chr9:137030029-137030040 chr9:137030028-137030040
24	E2F4	chr9:137029539-137030547	MCF10A-Er-Src	breast:	n/a	chr9:137030185-137030194 chr9:137030176-137030185 chr9:137030028-137030040 chr9:137030029-137030040
25	NFIC	chr9:137029436-137030279	HepG2	liver:	n/a	n/a
26	GTF3C2	chr9:137029942-137030788	K562	blood:	n/a	n/a
27	POLR2A	chr9:137029904-137030611	HepG2	liver:	n/a	n/a
28	BCLAF1	chr9:137029638-137030253	K562	blood:	n/a	chr9:137030050-137030059
29	EP300	chr9:137029515-137030307	A549	lung:	n/a	chr9:137030168-137030177 chr9:137030107-137030114 chr9:137030185-137030194
30	FOS	chr9:137029679-137030258	K562	blood:	n/a	n/a
31	NFYA	chr9:137029346-137030370	Hela-S3	cervix:	n/a	chr9:137029903-137029916 chr9:137030064-137030077
32	ELF1	chr9:137029682-137030745	GM12878	blood:	n/a	chr9:137030187-137030199 chr9:137030105-137030118
33	POLR2A	chr9:137029526-137030898	H1-neurons	neurons:	n/a	n/a
34	CEBPB	chr9:137029343-137030270	GM12878	blood:	n/a	n/a
35	TAF1	chr9:137029610-137030384	PFSK-1	brain:	n/a	n/a
36	CHD2	chr9:137029513-137030734	Hela-S3	cervix:	n/a	n/a
37	BRCA1	chr9:137029542-137030280	H1-hESC	embryonic stem cell:	n/a	n/a
38	RFX5	chr9:137029686-137030285	HepG2	liver:	n/a	n/a
39	ATF3	chr9:137030037-137030387	K562	blood:	n/a	chr9:137030183-137030192
40	MAX	chr9:137029557-137030872	H1-hESC	embryonic stem cell:	n/a	chr9:137030658-137030668
41	NFYB	chr9:137029524-137030342	K562	blood:	n/a	chr9:137029903-137029916 chr9:137030064-137030077 chr9:137029900-137029915
42	NFYA	chr9:137029672-137030209	GM12878	blood:	n/a	chr9:137029903-137029916 chr9:137030064-137030077
43	NFIC	chr9:137029439-137030267	GM12878	blood:	n/a	n/a
44	SETDB1	chr9:137028976-137030885	U2OS	brain:	n/a	chr9:137030176-137030185
45	REST	chr9:137029988-137030477	PFSK-1	brain:	n/a	n/a
46	MYC	chr9:137029559-137031082	NB4	blood:	n/a	chr9:137030658-137030668
47	ETS1	chr9:137029456-137030175	A549	lung:	n/a	chr9:137029931-137029938 chr9:137029928-137029941 chr9:137030104-137030114
48	JUND	chr9:137029853-137030234	HepG2	liver:	n/a	n/a
49	CREB1	chr9:137029876-137030214	A549	lung:	n/a	n/a
50	POLR2A	chr9:137029974-137030421	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:137030110..137032230-chr9:137037095..137040393,3	MCF-7	breast:
2	chr9:137003283..137007180-chr9:137027026..137030232,3	K562	blood:
3	chr9:136999027..137003702-chr9:137026566..137032835,8	MCF-7	breast:
4	chr9:137028457..137030780-chr9:137033087..137036645,3	MCF-7	breast:
5	chr9:136999035..137002778-chr9:137027888..137031331,5	K562	blood:
6	chr19:47291437..47292002-chr9:137029304..137030259,2	NB4	blood:
7	chr9:137029897..137032228-chr9:137170817..137173611,2	MCF-7	breast:
8	chr9:137028543..137032380-chr9:137216254..137220347,4	K562	blood:
9	chr9:137028191..137030569-chr9:137216306..137218797,3	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:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-WDR5-4	chr9:137029881-137030348	NONHSAT135378

Variant related genes	Relation type
RNU6ATAC	TF binding region
ENSG00000273473	TF binding region
ENSG00000196363	Chromatin interaction
ENSG00000273249	Chromatin interaction
ENSG00000186350	Chromatin interaction
ENSG00000273473	Chromatin interaction
ENSG00000105281	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1128044	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs28415637	0.90[AFR][1000 genomes]
rs28475221	0.90[AFR][1000 genomes]
rs28477532	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28490920	0.90[AFR][1000 genomes]
rs28498266	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28508246	0.90[AFR][1000 genomes]
rs28526200	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28549758	0.90[AFR][1000 genomes]
rs28588875	0.90[AFR][1000 genomes]
rs28611335	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28637447	0.81[AFR][1000 genomes]
rs28648812	0.90[AFR][1000 genomes]
rs28695913	0.90[AFR][1000 genomes]
rs35715743	0.90[AFR][1000 genomes]
rs35949820	0.86[AFR][1000 genomes]
rs36185416	0.91[AFR][1000 genomes];0.80[AMR][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	chr9:137015800-137030200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:137027600-137030200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr9:137028000-137030600	Active TSS	H1 Cell Line	embryonic stem cell
4	chr9:137028000-137031200	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr9:137028200-137030400	Active TSS	Primary T cells from cord blood	blood
6	chr9:137028200-137030400	Active TSS	Brain Anterior Caudate	brain
7	chr9:137028200-137030400	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr9:137028200-137030400	Active TSS	Fetal Brain Female	brain
9	chr9:137028200-137030600	Active TSS	H9 Cell Line	embryonic stem cell
10	chr9:137028200-137030600	Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr9:137028200-137030600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr9:137028200-137030600	Active TSS	Brain Angular Gyrus	brain
13	chr9:137028200-137030600	Active TSS	Brain Hippocampus Middle	brain
14	chr9:137028200-137030600	Active TSS	Colon Smooth Muscle	Colon
15	chr9:137028200-137031000	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr9:137028200-137031000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr9:137028200-137031000	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr9:137028200-137031000	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr9:137028200-137031000	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr9:137028200-137031200	Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr9:137028400-137030200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr9:137028400-137030200	Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr9:137028400-137030200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr9:137028400-137030200	Active TSS	Thymus	Thymus
25	chr9:137028400-137030400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr9:137028400-137030400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
27	chr9:137028400-137030400	Active TSS	Brain Cingulate Gyrus	brain
28	chr9:137028400-137030400	Active TSS	Placenta Amnion	Placenta Amnion
29	chr9:137028400-137030400	Active TSS	Right Atrium	heart
30	chr9:137028400-137030400	Active TSS	Osteobl	bone
31	chr9:137028400-137030600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr9:137028400-137030600	Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr9:137028400-137030600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr9:137028400-137030600	Active TSS	Fetal Kidney	kidney
35	chr9:137028400-137030600	Active TSS	Psoas Muscle	Psoas
36	chr9:137028400-137030600	Active TSS	NHLF	lung
37	chr9:137028400-137031000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr9:137028600-137030400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr9:137028600-137030400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr9:137028600-137030400	Active TSS	Fetal Lung	lung
41	chr9:137028600-137030400	Active TSS	Fetal Stomach	stomach
42	chr9:137028600-137030400	Active TSS	Left Ventricle	heart
43	chr9:137028600-137030400	Active TSS	Right Ventricle	heart
44	chr9:137028600-137030600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr9:137028600-137030600	Active TSS	Primary T helper naive cells from peripheral blood	blood
46	chr9:137028600-137030600	Active TSS	Brain Substantia Nigra	brain
47	chr9:137028600-137030600	Active TSS	Ovary	ovary
48	chr9:137028600-137030600	Active TSS	Rectal Smooth Muscle	rectum
49	chr9:137028600-137030600	Active TSS	HSMM	muscle
50	chr9:137028600-137031000	Active TSS	ES-WA7 Cell Line	embryonic stem cell

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