Variant report

Variant	rs28473171
Chromosome Location	chr9:137028987-137028988
allele	C/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	CTCF	chr9:137028940-137029090	HRPEpiC	eye:	n/a	n/a
4	POLR2A	chr9:137028859-137029196	Hela-S3	cervix:	n/a	n/a
5	SMARCB1	chr9:137028418-137029376	Hela-S3	cervix:	n/a	n/a
6	TCF7L2	chr9:137028865-137030362	Hela-S3	cervix:	n/a	n/a
7	ELF1	chr9:137028386-137029354	GM12878	blood:	n/a	n/a
8	CTCF	chr9:137028900-137029050	GM12867	blood:	n/a	n/a
9	CTCF	chr9:137028840-137028990	HMEC	breast:	n/a	n/a
10	PAX5	chr9:137028514-137029181	GM12892	blood:	n/a	n/a
11	ZNF143	chr9:137028981-137029129	Hela-S3	cervix:	n/a	n/a
12	SETDB1	chr9:137028976-137030885	U2OS	brain:	n/a	chr9:137030176-137030185
13	TBL1XR1	chr9:137028941-137029290	GM12878	blood:	n/a	n/a
14	TCF7L2	chr9:137028853-137029402	PANC-1	pancreas:	n/a	n/a
15	POLR2A	chr9:137028450-137029214	GM12878	blood:	n/a	n/a
16	POLR2A	chr9:137028481-137030843	GM18505	blood:	n/a	n/a
17	POLR2A	chr9:137028905-137029309	Hela-S3	cervix:	n/a	n/a
18	MXI1	chr9:137028828-137029298	GM12878	blood:	n/a	n/a
19	POLR2A	chr9:137028909-137029207	GM12878	blood:	n/a	n/a
20	CTCF	chr9:137028960-137029110	GM12872	blood:	n/a	n/a
21	CTCF	chr9:137028840-137028990	HCPEpiC	choroid plexus:	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	MAZ	chr9:137028927-137029229	Hela-S3	cervix:	n/a	n/a
25	ZNF143	chr9:137028767-137029181	GM12878	blood:	n/a	n/a
26	TFAP2C	chr9:137028673-137030757	Hela-S3	cervix:	n/a	chr9:137029619-137029634
27	POLR2A	chr9:137028947-137029009	GM12878	blood:	n/a	n/a
28	GATA1	chr9:137028746-137030407	PBDE	blood:	n/a	chr9:137029211-137029232
29	CHD2	chr9:137028692-137029245	Hela-S3	cervix:	n/a	chr9:137028759-137028769
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	MXI1	chr9:137028963-137029146	Hela-S3	cervix:	n/a	n/a
34	RUNX3	chr9:137028887-137030520	GM12878	blood:	n/a	chr9:137029806-137029815 chr9:137029806-137029815
35	YY1	chr9:137028895-137029831	GM12878	blood:	n/a	n/a
36	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
37	CHD1	chr9:137028966-137029263	GM12878	blood:	n/a	n/a
38	POLR2A	chr9:137028244-137030593	HUVEC	blood vessel:	n/a	n/a
39	HCFC1	chr9:137028410-137031485	Hela-S3	cervix:	n/a	n/a
40	RCOR1	chr9:137028875-137030465	Hela-S3	cervix:	n/a	n/a
41	JUND	chr9:137028929-137030343	Hela-S3	cervix:	n/a	n/a
42	MAZ	chr9:137028954-137029107	GM12878	blood:	n/a	n/a
43	POLR2A	chr9:137028450-137030934	GM12878	blood:	n/a	n/a
44	HMGN3	chr9:137028710-137029171	K562	blood:	n/a	n/a
45	RFX5	chr9:137028937-137030501	Hela-S3	cervix:	n/a	n/a
46	CTCF	chr9:137028960-137029110	HUVEC	blood vessel:	n/a	n/a
47	CTCF	chr9:137028900-137029050	NHLF	lung:	n/a	n/a
48	POLR2A	chr9:137028694-137029849	Hela-S3	cervix:	n/a	n/a
49	RUNX3	chr9:137028799-137030805	GM12878	blood:	n/a	chr9:137029806-137029815 chr9:137029806-137029815
50	MAX	chr9:137028746-137029279	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:137003283..137007180-chr9:137027026..137030232,3	K562	blood:
2	chr9:136999027..137003702-chr9:137026566..137032835,8	MCF-7	breast:
3	chr9:137028457..137030780-chr9:137033087..137036645,3	MCF-7	breast:
4	chr9:137028036..137029571-chr9:137206242..137207839,2	MCF-7	breast:
5	chr9:136999035..137002778-chr9:137027888..137031331,5	K562	blood:
6	chr9:137028543..137032380-chr9:137216254..137220347,4	K562	blood:
7	chr9:137028191..137030569-chr9:137216306..137218797,3	MCF-7	breast:
8	chr9:137028413..137030043-chr9:137217390..137219044,2	K562	blood:
9	chr9:137028423..137041755-chr9:137210581..137221866,35	MCF-7	breast:
10	chr9:137028231..137030926-chr9:137032684..137034391,3	K562	blood:

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

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs28360858	1.00[EUR][1000 genomes]
rs28399690	1.00[EUR][1000 genomes]
rs28401385	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28412245	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28440102	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28442241	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs28452481	1.00[EUR][1000 genomes]
rs28479377	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28491791	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28507057	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28510444	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs28523906	0.83[AFR][1000 genomes]
rs28562957	1.00[EUR][1000 genomes]
rs28572025	0.84[AFR][1000 genomes]
rs28579703	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28620240	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28626222	0.83[AFR][1000 genomes]
rs28637761	0.85[AFR][1000 genomes]
rs28705689	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28705949	0.86[AFR][1000 genomes]
rs28708401	1.00[EUR][1000 genomes]
rs28710163	1.00[EUR][1000 genomes]
rs28712382	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28714237	1.00[EUR][1000 genomes]
rs28740804	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28758854	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28759300	0.83[AFR][1000 genomes]
rs28759311	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34062061	0.82[AFR][1000 genomes]
rs34079254	1.00[EUR][1000 genomes]
rs34194763	1.00[EUR][1000 genomes]
rs34473303	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34546899	1.00[EUR][1000 genomes]
rs34607253	0.92[EUR][1000 genomes]
rs34646496	1.00[EUR][1000 genomes]
rs34861636	1.00[EUR][1000 genomes]
rs34929179	1.00[EUR][1000 genomes]
rs35209649	1.00[EUR][1000 genomes]
rs35322411	1.00[EUR][1000 genomes]
rs35387289	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35419030	1.00[EUR][1000 genomes]
rs35448798	1.00[EUR][1000 genomes]
rs35487246	0.84[EUR][1000 genomes]
rs35489314	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35504753	1.00[EUR][1000 genomes]
rs35511305	1.00[EUR][1000 genomes]
rs35709000	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35726748	1.00[EUR][1000 genomes]
rs35924689	1.00[EUR][1000 genomes]
rs71483222	1.00[EUR][1000 genomes]
rs71505283	1.00[EUR][1000 genomes]
rs71505284	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	chr9:137015800-137030200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:137016400-137029600	Weak transcription	K562	blood
3	chr9:137024000-137029000	Weak transcription	A549	lung
4	chr9:137026400-137029000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr9:137027600-137029400	Enhancers	Fetal Brain Male	brain
6	chr9:137027600-137029600	Enhancers	HepG2	liver
7	chr9:137027600-137030200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr9:137027800-137029200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
9	chr9:137027800-137029600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
10	chr9:137028000-137029000	Flanking Active TSS	Fetal Intestine Small	intestine
11	chr9:137028000-137029200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr9:137028000-137029200	Flanking Active TSS	Colonic Mucosa	Colon
13	chr9:137028000-137029200	Flanking Active TSS	Duodenum Mucosa	Duodenum
14	chr9:137028000-137029200	Flanking Active TSS	Fetal Intestine Large	intestine
15	chr9:137028000-137029200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
16	chr9:137028000-137029400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr9:137028000-137029600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr9:137028000-137029600	Flanking Active TSS	Stomach Smooth Muscle	stomach
19	chr9:137028000-137030600	Active TSS	H1 Cell Line	embryonic stem cell
20	chr9:137028000-137031200	Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr9:137028200-137029000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
22	chr9:137028200-137029000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
23	chr9:137028200-137029000	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr9:137028200-137029000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
25	chr9:137028200-137029200	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr9:137028200-137029200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
27	chr9:137028200-137029200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr9:137028200-137029200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr9:137028200-137029200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
30	chr9:137028200-137029200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr9:137028200-137029200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr9:137028200-137029200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr9:137028200-137029200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
34	chr9:137028200-137029200	Flanking Active TSS	Fetal Muscle Leg	muscle
35	chr9:137028200-137029600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
36	chr9:137028200-137029600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
37	chr9:137028200-137029600	Flanking Active TSS	Placenta	Placenta
38	chr9:137028200-137029800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
39	chr9:137028200-137030400	Active TSS	Primary T cells from cord blood	blood
40	chr9:137028200-137030400	Active TSS	Brain Anterior Caudate	brain
41	chr9:137028200-137030400	Active TSS	Brain Inferior Temporal Lobe	brain
42	chr9:137028200-137030400	Active TSS	Fetal Brain Female	brain
43	chr9:137028200-137030600	Active TSS	H9 Cell Line	embryonic stem cell
44	chr9:137028200-137030600	Active TSS	iPS-18 Cell Line	embryonic stem cell
45	chr9:137028200-137030600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr9:137028200-137030600	Active TSS	Brain Angular Gyrus	brain
47	chr9:137028200-137030600	Active TSS	Brain Hippocampus Middle	brain
48	chr9:137028200-137030600	Active TSS	Colon Smooth Muscle	Colon
49	chr9:137028200-137031000	Active TSS	ES-I3 Cell Line	embryonic stem cell
50	chr9:137028200-137031000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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