Variant report

Variant	rs28637761
Chromosome Location	chr9:137029148-137029149
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	MAFK	chr9:137028976-137029175	Hela-S3	cervix:	n/a	n/a
2	GTF3C2	chr9:137028928-137030946	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr9:137028859-137029196	Hela-S3	cervix:	n/a	n/a
4	SMARCB1	chr9:137028418-137029376	Hela-S3	cervix:	n/a	n/a
5	TCF7L2	chr9:137028865-137030362	Hela-S3	cervix:	n/a	n/a
6	ELF1	chr9:137028386-137029354	GM12878	blood:	n/a	n/a
7	TCF7L2	chr9:137029058-137029349	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr9:137029011-137029253	Hela-S3	cervix:	n/a	n/a
9	PAX5	chr9:137028514-137029181	GM12892	blood:	n/a	n/a
10	SETDB1	chr9:137028976-137030885	U2OS	brain:	n/a	chr9:137030176-137030185
11	TBL1XR1	chr9:137028941-137029290	GM12878	blood:	n/a	n/a
12	TCF7L2	chr9:137028853-137029402	PANC-1	pancreas:	n/a	n/a
13	KAP1	chr9:137029034-137030794	U2OS	brain:	n/a	n/a
14	POLR2A	chr9:137028450-137029214	GM12878	blood:	n/a	n/a
15	POLR2A	chr9:137028481-137030843	GM18505	blood:	n/a	n/a
16	KAP1	chr9:137029093-137030169	K562	blood:	n/a	n/a
17	GATA2	chr9:137029025-137030042	HUVEC	blood vessel:	n/a	chr9:137029211-137029232
18	POLR2A	chr9:137028905-137029309	Hela-S3	cervix:	n/a	n/a
19	BRCA1	chr9:137029043-137030497	Hela-S3	cervix:	n/a	n/a
20	MXI1	chr9:137028828-137029298	GM12878	blood:	n/a	n/a
21	POLR2A	chr9:137028909-137029207	GM12878	blood:	n/a	n/a
22	POLR2A	chr9:137028437-137030891	GM19099	blood:	n/a	n/a
23	MAX	chr9:137028694-137030859	Hela-S3	cervix:	n/a	chr9:137030658-137030668
24	CTCF	chr9:137029080-137029230	HUVEC	blood vessel:	n/a	n/a
25	MAZ	chr9:137028927-137029229	Hela-S3	cervix:	n/a	n/a
26	MYC	chr9:137028992-137030911	Hela-S3	cervix:	n/a	chr9:137030658-137030668
27	ZNF143	chr9:137028767-137029181	GM12878	blood:	n/a	n/a
28	TFAP2C	chr9:137028673-137030757	Hela-S3	cervix:	n/a	chr9:137029619-137029634
29	YY1	chr9:137029109-137029766	GM12892	blood:	n/a	n/a
30	GATA1	chr9:137028746-137030407	PBDE	blood:	n/a	chr9:137029211-137029232
31	CHD2	chr9:137028692-137029245	Hela-S3	cervix:	n/a	chr9:137028759-137028769
32	POLR2A	chr9:137028444-137030838	GM18526	blood:	n/a	n/a
33	CTCF	chr9:137029000-137029150	AG04449	skin:	n/a	n/a
34	POLR2A	chr9:137028462-137030780	GM19193	blood:	n/a	n/a
35	CTCF	chr9:137029020-137029170	AG10803	skin:	n/a	n/a
36	KAP1	chr9:137028873-137030941	HEK293	kidney:	n/a	n/a
37	RUNX3	chr9:137028887-137030520	GM12878	blood:	n/a	chr9:137029806-137029815 chr9:137029806-137029815
38	YY1	chr9:137028895-137029831	GM12878	blood:	n/a	n/a
39	SMC3	chr9:137029001-137029238	Hela-S3	cervix:	n/a	n/a
40	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
41	CHD1	chr9:137028966-137029263	GM12878	blood:	n/a	n/a
42	POLR2A	chr9:137028244-137030593	HUVEC	blood vessel:	n/a	n/a
43	HCFC1	chr9:137028410-137031485	Hela-S3	cervix:	n/a	n/a
44	CTCF	chr9:137029000-137029150	GM12873	blood:	n/a	n/a
45	RCOR1	chr9:137028875-137030465	Hela-S3	cervix:	n/a	n/a
46	GATA2	chr9:137028999-137029383	SH-SY5Y	brain:	n/a	chr9:137029211-137029232
47	JUND	chr9:137028929-137030343	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr9:137028450-137030934	GM12878	blood:	n/a	n/a
49	HMGN3	chr9:137028710-137029171	K562	blood:	n/a	n/a
50	RFX5	chr9:137028937-137030501	Hela-S3	cervix:	n/a	n/a

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	chr9:137028543..137032380-chr9:137216254..137220347,4	K562	blood:
8	chr9:137028191..137030569-chr9:137216306..137218797,3	MCF-7	breast:
9	chr9:137028413..137030043-chr9:137217390..137219044,2	K562	blood:
10	chr9:137028423..137041755-chr9:137210581..137221866,35	MCF-7	breast:
11	chr9:137028231..137030926-chr9:137032684..137034391,3	K562	blood:

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

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs17151353	1.00[MEX][hapmap]
rs28401385	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs28412245	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs28440102	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs28442241	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs28473171	0.85[AFR][1000 genomes]
rs28479377	0.92[AFR][1000 genomes]
rs28491791	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs28507057	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs28510444	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs28523906	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28572025	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28578388	0.85[AMR][1000 genomes]
rs28579703	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs28590546	0.85[AMR][1000 genomes]
rs28620240	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs28626222	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28637077	1.00[AMR][1000 genomes]
rs28657551	1.00[AMR][1000 genomes]
rs28705689	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs28705949	0.85[AFR][1000 genomes]
rs28712382	1.00[ASW][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs28726357	1.00[AMR][1000 genomes]
rs28758854	1.00[ASW][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs28759300	0.83[AFR][1000 genomes]
rs28759311	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs34062061	0.82[AFR][1000 genomes]
rs34473303	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs35387289	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs35489314	0.92[AFR][1000 genomes]
rs35709000	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs58124205	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58577872	0.85[AMR][1000 genomes]
rs58734062	1.00[AMR][1000 genomes]
rs73663023	0.85[AMR][1000 genomes]
rs73663200	0.85[AFR][1000 genomes];1.00[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	chr9:137016400-137029600	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	chr9:137027800-137029200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
7	chr9:137027800-137029600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
8	chr9:137028000-137029200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr9:137028000-137029200	Flanking Active TSS	Colonic Mucosa	Colon
10	chr9:137028000-137029200	Flanking Active TSS	Duodenum Mucosa	Duodenum
11	chr9:137028000-137029200	Flanking Active TSS	Fetal Intestine Large	intestine
12	chr9:137028000-137029200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr9:137028000-137029400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr9:137028000-137029600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr9:137028000-137029600	Flanking Active TSS	Stomach Smooth Muscle	stomach
16	chr9:137028000-137030600	Active TSS	H1 Cell Line	embryonic stem cell
17	chr9:137028000-137031200	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr9:137028200-137029200	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr9:137028200-137029200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
20	chr9:137028200-137029200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr9:137028200-137029200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr9:137028200-137029200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
23	chr9:137028200-137029200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr9:137028200-137029200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr9:137028200-137029200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr9:137028200-137029200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
27	chr9:137028200-137029200	Flanking Active TSS	Fetal Muscle Leg	muscle
28	chr9:137028200-137029600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
29	chr9:137028200-137029600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
30	chr9:137028200-137029600	Flanking Active TSS	Placenta	Placenta
31	chr9:137028200-137029800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
32	chr9:137028200-137030400	Active TSS	Primary T cells from cord blood	blood
33	chr9:137028200-137030400	Active TSS	Brain Anterior Caudate	brain
34	chr9:137028200-137030400	Active TSS	Brain Inferior Temporal Lobe	brain
35	chr9:137028200-137030400	Active TSS	Fetal Brain Female	brain
36	chr9:137028200-137030600	Active TSS	H9 Cell Line	embryonic stem cell
37	chr9:137028200-137030600	Active TSS	iPS-18 Cell Line	embryonic stem cell
38	chr9:137028200-137030600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr9:137028200-137030600	Active TSS	Brain Angular Gyrus	brain
40	chr9:137028200-137030600	Active TSS	Brain Hippocampus Middle	brain
41	chr9:137028200-137030600	Active TSS	Colon Smooth Muscle	Colon
42	chr9:137028200-137031000	Active TSS	ES-I3 Cell Line	embryonic stem cell
43	chr9:137028200-137031000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr9:137028200-137031000	Active TSS	HUES48 Cell Line	embryonic stem cell
45	chr9:137028200-137031000	Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr9:137028200-137031000	Active TSS	iPS-15b Cell Line	embryonic stem cell
47	chr9:137028200-137031200	Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr9:137028400-137029200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr9:137028400-137029400	Active TSS	Small Intestine	intestine
50	chr9:137028400-137029600	Flanking Active TSS	Primary B cells from cord blood	blood

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