Variant report

Variant	rs28398408
Chromosome Location	chr9:137029346-137029347
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	GTF3C2	chr9:137028928-137030946	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr9:137029337-137029794	GM12892	blood:	n/a	n/a
3	SMARCB1	chr9:137028418-137029376	Hela-S3	cervix:	n/a	n/a
4	TCF7L2	chr9:137028865-137030362	Hela-S3	cervix:	n/a	n/a
5	ELF1	chr9:137028386-137029354	GM12878	blood:	n/a	n/a
6	TCF7L2	chr9:137029058-137029349	Hela-S3	cervix:	n/a	n/a
7	NFYA	chr9:137029346-137030370	Hela-S3	cervix:	n/a	chr9:137029903-137029916 chr9:137030064-137030077
8	CEBPB	chr9:137029343-137030270	GM12878	blood:	n/a	n/a
9	POLR2A	chr9:137029230-137029864	PANC-1	pancreas:	n/a	n/a
10	SETDB1	chr9:137028976-137030885	U2OS	brain:	n/a	chr9:137030176-137030185
11	TCF7L2	chr9:137028853-137029402	PANC-1	pancreas:	n/a	n/a
12	KAP1	chr9:137029034-137030794	U2OS	brain:	n/a	n/a
13	POLR2A	chr9:137028481-137030843	GM18505	blood:	n/a	n/a
14	KAP1	chr9:137029093-137030169	K562	blood:	n/a	n/a
15	GATA2	chr9:137029025-137030042	HUVEC	blood vessel:	n/a	chr9:137029211-137029232
16	BRCA1	chr9:137029043-137030497	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr9:137028437-137030891	GM19099	blood:	n/a	n/a
18	TEAD4	chr9:137029335-137030697	SK-N-SH	brain:	n/a	n/a
19	FOSL2	chr9:137029335-137030775	A549	lung:	n/a	n/a
20	MAX	chr9:137028694-137030859	Hela-S3	cervix:	n/a	chr9:137030658-137030668
21	POLR2A	chr9:137029327-137029881	GM12878	blood:	n/a	n/a
22	YY1	chr9:137029294-137030205	GM12878	blood:	n/a	chr9:137030118-137030129
23	POLR2A	chr9:137029231-137029855	GM12892	blood:	n/a	n/a
24	MYC	chr9:137028992-137030911	Hela-S3	cervix:	n/a	chr9:137030658-137030668
25	GABPA	chr9:137029335-137030728	A549	lung:	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
26	TFAP2C	chr9:137028673-137030757	Hela-S3	cervix:	n/a	chr9:137029619-137029634
27	POLR2A	chr9:137029249-137029800	GM12892	blood:	n/a	n/a
28	YY1	chr9:137029109-137029766	GM12892	blood:	n/a	n/a
29	GATA1	chr9:137028746-137030407	PBDE	blood:	n/a	chr9:137029211-137029232
30	POLR2A	chr9:137028444-137030838	GM18526	blood:	n/a	n/a
31	POLR2A	chr9:137028462-137030780	GM19193	blood:	n/a	n/a
32	KAP1	chr9:137028873-137030941	HEK293	kidney:	n/a	n/a
33	RPC155	chr9:137029330-137029997	Hela-S3	cervix:	n/a	n/a
34	POU2F2	chr9:137029334-137030339	GM12878	blood:	n/a	n/a
35	TBP	chr9:137029328-137030361	Hela-S3	cervix:	n/a	chr9:137029709-137029720
36	RUNX3	chr9:137028887-137030520	GM12878	blood:	n/a	chr9:137029806-137029815 chr9:137029806-137029815
37	YY1	chr9:137028895-137029831	GM12878	blood:	n/a	n/a
38	TFAP2A	chr9:137028666-137030831	Hela-S3	cervix:	n/a	chr9:137030499-137030509 chr9:137030376-137030384 chr9:137030483-137030491 chr9:137029240-137029251 chr9:137030499-137030509 chr9:137029240-137029251 chr9:137029240-137029251 chr9:137029241-137029249 chr9:137030497-137030511 chr9:137029242-137029250 chr9:137030376-137030384 chr9:137030499-137030509 chr9:137029242-137029250 chr9:137029241-137029249 chr9:137030499-137030511 chr9:137029239-137029253 chr9:137030376-137030384 chr9:137029240-137029251 chr9:137029242-137029250 chr9:137029241-137029249 chr9:137030499-137030509 chr9:137029239-137029254
39	POLR2A	chr9:137028244-137030593	HUVEC	blood vessel:	n/a	n/a
40	HCFC1	chr9:137028410-137031485	Hela-S3	cervix:	n/a	n/a
41	HEY1	chr9:137029296-137029821	K562	blood:	n/a	n/a
42	RCOR1	chr9:137028875-137030465	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr9:137029266-137031976	Raji	blood:	n/a	n/a
44	GATA2	chr9:137028999-137029383	SH-SY5Y	brain:	n/a	chr9:137029211-137029232
45	JUND	chr9:137028929-137030343	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr9:137028450-137030934	GM12878	blood:	n/a	n/a
47	SP1	chr9:137029337-137030788	A549	lung:	n/a	chr9:137030407-137030419 chr9:137029904-137029925 chr9:137030024-137030038
48	RFX5	chr9:137028937-137030501	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr9:137028694-137029849	Hela-S3	cervix:	n/a	n/a
50	RUNX3	chr9:137028799-137030805	GM12878	blood:	n/a	chr9:137029806-137029815 chr9:137029806-137029815

No.	Distal block	Cell Line	Cell type
1	chr9:137000678..137001573-chr9:137029002..137029689,2	Hela-S3	cervix:
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	chr9:137028036..137029571-chr9:137206242..137207839,2	MCF-7	breast:
6	chr9:136999035..137002778-chr9:137027888..137031331,5	K562	blood:
7	chr19:47291437..47292002-chr9:137029304..137030259,2	NB4	blood:
8	chr9:137028543..137032380-chr9:137216254..137220347,4	K562	blood:
9	chr9:137028191..137030569-chr9:137216306..137218797,3	MCF-7	breast:
10	chr9:137028413..137030043-chr9:137217390..137219044,2	K562	blood:
11	chr9:137028423..137041755-chr9:137210581..137221866,35	MCF-7	breast:
12	chr9:137028231..137030926-chr9:137032684..137034391,3	K562	blood:

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

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs28401669	0.87[ASN][1000 genomes]
rs28504693	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28549934	0.83[ASN][1000 genomes]
rs28650068	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs28703244	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28705314	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][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	chr9:137016400-137029600	Weak transcription	K562	blood
3	chr9:137027600-137029400	Enhancers	Fetal Brain Male	brain
4	chr9:137027600-137029600	Enhancers	HepG2	liver
5	chr9:137027600-137030200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr9:137027800-137029600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
7	chr9:137028000-137029400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr9:137028000-137029600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr9:137028000-137029600	Flanking Active TSS	Stomach Smooth Muscle	stomach
10	chr9:137028000-137030600	Active TSS	H1 Cell Line	embryonic stem cell
11	chr9:137028000-137031200	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr9:137028200-137029600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
13	chr9:137028200-137029600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
14	chr9:137028200-137029600	Flanking Active TSS	Placenta	Placenta
15	chr9:137028200-137029800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr9:137028200-137030400	Active TSS	Primary T cells from cord blood	blood
17	chr9:137028200-137030400	Active TSS	Brain Anterior Caudate	brain
18	chr9:137028200-137030400	Active TSS	Brain Inferior Temporal Lobe	brain
19	chr9:137028200-137030400	Active TSS	Fetal Brain Female	brain
20	chr9:137028200-137030600	Active TSS	H9 Cell Line	embryonic stem cell
21	chr9:137028200-137030600	Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr9:137028200-137030600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr9:137028200-137030600	Active TSS	Brain Angular Gyrus	brain
24	chr9:137028200-137030600	Active TSS	Brain Hippocampus Middle	brain
25	chr9:137028200-137030600	Active TSS	Colon Smooth Muscle	Colon
26	chr9:137028200-137031000	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr9:137028200-137031000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr9:137028200-137031000	Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr9:137028200-137031000	Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr9:137028200-137031000	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr9:137028200-137031200	Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr9:137028400-137029400	Active TSS	Small Intestine	intestine
33	chr9:137028400-137029600	Flanking Active TSS	Primary B cells from cord blood	blood
34	chr9:137028400-137029600	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chr9:137028400-137030200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr9:137028400-137030200	Active TSS	Primary T helper cells PMA-I stimulated	--
37	chr9:137028400-137030200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr9:137028400-137030200	Active TSS	Thymus	Thymus
39	chr9:137028400-137030400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr9:137028400-137030400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
41	chr9:137028400-137030400	Active TSS	Brain Cingulate Gyrus	brain
42	chr9:137028400-137030400	Active TSS	Placenta Amnion	Placenta Amnion
43	chr9:137028400-137030400	Active TSS	Right Atrium	heart
44	chr9:137028400-137030400	Active TSS	Osteobl	bone
45	chr9:137028400-137030600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr9:137028400-137030600	Active TSS	Primary T killer memory cells from peripheral blood	blood
47	chr9:137028400-137030600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr9:137028400-137030600	Active TSS	Fetal Kidney	kidney
49	chr9:137028400-137030600	Active TSS	Psoas Muscle	Psoas
50	chr9:137028400-137030600	Active TSS	NHLF	lung

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