Variant report

Variant	rs73837574
Chromosome Location	chr3:52506062-52506063
allele	C/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	RAD21	chr3:52505980-52506342	H1-hESC	embryonic stem cell:	n/a	chr3:52506153-52506163 chr3:52506148-52506167 chr3:52506151-52506164
2	CTCF	chr3:52506025-52506224	SK-N-SH_RA	brain:	n/a	chr3:52506150-52506163 chr3:52506148-52506164 chr3:52506152-52506162 chr3:52506149-52506170 chr3:52506150-52506159 chr3:52506147-52506165
3	CTCF	chr3:52506010-52506312	GM12878	blood:	n/a	chr3:52506150-52506163 chr3:52506148-52506164 chr3:52506152-52506162 chr3:52506149-52506170 chr3:52506150-52506159 chr3:52506147-52506165
4	CTCF	chr3:52506024-52506285	Kidney_OC	kidney:	n/a	chr3:52506150-52506163 chr3:52506148-52506164 chr3:52506152-52506162 chr3:52506149-52506170 chr3:52506150-52506159 chr3:52506147-52506165
5	CTCF	chr3:52506060-52506210	NHEK	skin:	n/a	chr3:52506150-52506163 chr3:52506148-52506164 chr3:52506152-52506162 chr3:52506149-52506170 chr3:52506150-52506159 chr3:52506147-52506165
6	SMC3	chr3:52506001-52506272	K562	blood:	n/a	chr3:52506149-52506163 chr3:52506153-52506163
7	CTCF	chr3:52506047-52506265	K562	blood:	n/a	chr3:52506150-52506163 chr3:52506148-52506164 chr3:52506152-52506162 chr3:52506149-52506170 chr3:52506150-52506159 chr3:52506147-52506165
8	SMC3	chr3:52506014-52506335	Hela-S3	cervix:	n/a	chr3:52506149-52506163 chr3:52506153-52506163
9	CTCF	chr3:52505803-52506317	GM12891	blood:	n/a	chr3:52506150-52506163 chr3:52506148-52506164 chr3:52506152-52506162 chr3:52506149-52506170 chr3:52506150-52506159 chr3:52506147-52506165
10	CTCF	chr3:52506060-52506210	HEEpiC	esophagus:	n/a	chr3:52506150-52506163 chr3:52506148-52506164 chr3:52506152-52506162 chr3:52506149-52506170 chr3:52506150-52506159 chr3:52506147-52506165
11	CTCF	chr3:52506060-52506210	HepG2	liver:	n/a	chr3:52506150-52506163 chr3:52506148-52506164 chr3:52506152-52506162 chr3:52506149-52506170 chr3:52506150-52506159 chr3:52506147-52506165
12	CTCF	chr3:52506060-52506210	HPF	lung:	n/a	chr3:52506150-52506163 chr3:52506148-52506164 chr3:52506152-52506162 chr3:52506149-52506170 chr3:52506150-52506159 chr3:52506147-52506165
13	CTCF	chr3:52505974-52506244	H1-hESC	embryonic stem cell:	n/a	chr3:52506150-52506163 chr3:52506148-52506164 chr3:52506152-52506162 chr3:52506149-52506170 chr3:52506150-52506159 chr3:52506147-52506165
14	RAD21	chr3:52505911-52506421	A549	lung:	n/a	chr3:52506153-52506163 chr3:52506148-52506167 chr3:52506151-52506164
15	RAD21	chr3:52505798-52506521	HCT-116	colon:	n/a	chr3:52506153-52506163 chr3:52506148-52506167 chr3:52506151-52506164
16	CTCF	chr3:52506060-52506210	GM12864	blood:	n/a	chr3:52506150-52506163 chr3:52506148-52506164 chr3:52506152-52506162 chr3:52506149-52506170 chr3:52506150-52506159 chr3:52506147-52506165
17	SMC3	chr3:52505993-52506353	HepG2	liver:	n/a	chr3:52506149-52506163 chr3:52506153-52506163
18	RAD21	chr3:52505923-52506432	H1-hESC	embryonic stem cell:	n/a	chr3:52506153-52506163 chr3:52506148-52506167 chr3:52506151-52506164
19	RAD21	chr3:52505729-52506647	SK-N-SH	brain:	n/a	chr3:52506153-52506163 chr3:52506148-52506167 chr3:52506151-52506164
20	CTCF	chr3:52506043-52506264	GM13977	blood:	n/a	chr3:52506150-52506163 chr3:52506148-52506164 chr3:52506152-52506162 chr3:52506149-52506170 chr3:52506150-52506159 chr3:52506147-52506165
21	CTCF	chr3:52506060-52506210	GM12870	blood:	n/a	chr3:52506150-52506163 chr3:52506148-52506164 chr3:52506152-52506162 chr3:52506149-52506170 chr3:52506150-52506159 chr3:52506147-52506165
22	CTCF	chr3:52506023-52506278	H1-hESC	embryonic stem cell:	n/a	chr3:52506150-52506163 chr3:52506148-52506164 chr3:52506152-52506162 chr3:52506149-52506170 chr3:52506150-52506159 chr3:52506147-52506165
23	CTCF	chr3:52506060-52506210	GM06990	blood:	n/a	chr3:52506150-52506163 chr3:52506148-52506164 chr3:52506152-52506162 chr3:52506149-52506170 chr3:52506150-52506159 chr3:52506147-52506165
24	POLR2A	chr3:52505992-52506208	HUVEC	blood vessel:	n/a	n/a
25	CTCF	chr3:52506038-52506271	Gliobla	brain:	n/a	chr3:52506150-52506163 chr3:52506148-52506164 chr3:52506152-52506162 chr3:52506149-52506170 chr3:52506150-52506159 chr3:52506147-52506165
26	RAD21	chr3:52505901-52506404	A549	lung:	n/a	chr3:52506153-52506163 chr3:52506148-52506167 chr3:52506151-52506164
27	CTCF	chr3:52505998-52506312	GM19239	blood:	n/a	chr3:52506150-52506163 chr3:52506148-52506164 chr3:52506152-52506162 chr3:52506149-52506170 chr3:52506150-52506159 chr3:52506147-52506165
28	CTCF	chr3:52506045-52506244	SK-N-SH_RA	brain:	n/a	chr3:52506150-52506163 chr3:52506148-52506164 chr3:52506152-52506162 chr3:52506149-52506170 chr3:52506150-52506159 chr3:52506147-52506165
29	CTCF	chr3:52505995-52506317	GM19238	blood:	n/a	chr3:52506150-52506163 chr3:52506148-52506164 chr3:52506152-52506162 chr3:52506149-52506170 chr3:52506150-52506159 chr3:52506147-52506165
30	CTCF	chr3:52506006-52506292	MCF-7	breast:	n/a	chr3:52506150-52506163 chr3:52506148-52506164 chr3:52506152-52506162 chr3:52506149-52506170 chr3:52506150-52506159 chr3:52506147-52506165
31	POLR2A	chr3:52505839-52506172	MCF-7	breast:	n/a	n/a
32	MXI1	chr3:52505961-52506576	SK-N-SH	brain:	n/a	n/a
33	ZNF143	chr3:52506049-52506260	K562	blood:	n/a	n/a
34	CTCF	chr3:52505994-52506301	MCF-7	breast:	n/a	chr3:52506150-52506163 chr3:52506148-52506164 chr3:52506152-52506162 chr3:52506149-52506170 chr3:52506150-52506159 chr3:52506147-52506165
35	CTCF	chr3:52505983-52506321	K562	blood:	n/a	chr3:52506150-52506163 chr3:52506148-52506164 chr3:52506152-52506162 chr3:52506149-52506170 chr3:52506150-52506159 chr3:52506147-52506165
36	SIN3A	chr3:52506051-52506334	H1-hESC	embryonic stem cell:	n/a	n/a
37	RUNX3	chr3:52505975-52506313	GM12878	blood:	n/a	n/a
38	RAD21	chr3:52506025-52506359	GM12878	blood:	n/a	chr3:52506153-52506163 chr3:52506148-52506167 chr3:52506151-52506164
39	RAD21	chr3:52506034-52506331	GM12878	blood:	n/a	chr3:52506153-52506163 chr3:52506148-52506167 chr3:52506151-52506164
40	RAD21	chr3:52505948-52506330	SK-N-SH_RA	brain:	n/a	chr3:52506153-52506163 chr3:52506148-52506167 chr3:52506151-52506164
41	RAD21	chr3:52505993-52506357	Hela-S3	cervix:	n/a	chr3:52506153-52506163 chr3:52506148-52506167 chr3:52506151-52506164
42	CTCF	chr3:52506000-52506150	HEK293	kidney:	n/a	n/a
43	CTCF	chr3:52505960-52506369	HepG2	liver:	n/a	chr3:52506150-52506163 chr3:52506148-52506164 chr3:52506152-52506162 chr3:52506149-52506170 chr3:52506150-52506159 chr3:52506147-52506165
44	ZNF143	chr3:52505976-52506319	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr3:52505971-52506167	MCF-7	breast:	n/a	n/a
46	CTCF	chr3:52505997-52506297	GM19240	blood:	n/a	chr3:52506150-52506163 chr3:52506148-52506164 chr3:52506152-52506162 chr3:52506149-52506170 chr3:52506150-52506159 chr3:52506147-52506165
47	POLR2A	chr3:52506001-52506310	HUVEC	blood vessel:	n/a	n/a
48	CTCF	chr3:52505915-52506438	MCF-7	breast:	n/a	chr3:52506150-52506163 chr3:52506148-52506164 chr3:52506152-52506162 chr3:52506149-52506170 chr3:52506150-52506159 chr3:52506147-52506165
49	RUNX3	chr3:52506022-52506277	GM12878	blood:	n/a	n/a
50	CTCF	chr3:52506056-52506318	A549	lung:	n/a	chr3:52506150-52506163 chr3:52506148-52506164 chr3:52506152-52506162 chr3:52506149-52506170 chr3:52506150-52506159 chr3:52506147-52506165

No.	Distal block	Cell Line	Cell type
1	chr3:52505487..52507011-chr3:52517843..52519757,2	K562	blood:
2	chr3:52487939..52491238-chr3:52504089..52507877,6	MCF-7	breast:
3	chr3:52505024..52507887-chr3:52527744..52529874,2	MCF-7	breast:
4	chr3:52488681..52492997-chr3:52505692..52511376,6	K562	blood:
5	chr3:52503525..52506168-chr3:52566167..52568849,2	MCF-7	breast:
6	chr3:52505027..52507504-chr3:52738535..52741338,2	MCF-7	breast:
7	chr3:52504996..52506918-chr3:52535565..52538055,2	MCF-7	breast:
8	chr3:52504515..52506973-chr3:52565446..52568302,2	MCF-7	breast:

Variant related genes	Relation type
NISCH	TF binding region
ENSG00000010327	Chromatin interaction
ENSG00000168268	Chromatin interaction
ENSG00000114854	Chromatin interaction
ENSG00000010322	Chromatin interaction
ENSG00000016864	Chromatin interaction
ENSG00000168273	Chromatin interaction
ENSG00000114902	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs55931436	1.00[AMR][1000 genomes]
rs56263308	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56326215	1.00[AFR][1000 genomes]
rs56332579	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60063053	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61589587	1.00[AMR][1000 genomes]
rs61734625	1.00[AMR][1000 genomes]
rs61738522	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6765965	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6776645	1.00[AMR][1000 genomes]
rs6778451	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6789826	1.00[AMR][1000 genomes]
rs73835711	1.00[AMR][1000 genomes]
rs73835763	1.00[AMR][1000 genomes]
rs73835764	1.00[AMR][1000 genomes]
rs73835767	1.00[AMR][1000 genomes]
rs73835769	1.00[AMR][1000 genomes]
rs73835772	1.00[AMR][1000 genomes]
rs73835773	1.00[AMR][1000 genomes]
rs73835774	1.00[AMR][1000 genomes]
rs73837050	1.00[AMR][1000 genomes]
rs73837051	1.00[AMR][1000 genomes]
rs73837056	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73837058	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73838346	1.00[AMR][1000 genomes]
rs73838349	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	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
3	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv876793	chr3:52450043-52584787	Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	esv1818902	chr3:52481406-52572056	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52491600-52509400	Weak transcription	Small Intestine	intestine
2	chr3:52491600-52528000	Strong transcription	Thymus	Thymus
3	chr3:52491800-52506400	Weak transcription	Stomach Mucosa	stomach
4	chr3:52491800-52517200	Strong transcription	Fetal Stomach	stomach
5	chr3:52491800-52524000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:52491800-52527000	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr3:52491800-52528200	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:52491800-52528200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:52492000-52516800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:52492000-52517200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:52492200-52506200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr3:52492400-52517400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:52493000-52506800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr3:52493000-52527800	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr3:52493200-52507000	Strong transcription	Fetal Thymus	thymus
16	chr3:52493400-52506400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr3:52495400-52507600	Weak transcription	Fetal Kidney	kidney
18	chr3:52495600-52506200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr3:52498000-52506400	Weak transcription	Primary hematopoietic stem cells	blood
20	chr3:52498600-52527200	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr3:52499200-52517200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr3:52499400-52527800	Strong transcription	Primary T cells from cord blood	blood
23	chr3:52499600-52529200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr3:52499800-52507200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr3:52500200-52517000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:52501000-52515200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr3:52501600-52528800	Strong transcription	Fetal Intestine Small	intestine
28	chr3:52502800-52506400	Weak transcription	NHDF-Ad	bronchial
29	chr3:52502800-52517200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr3:52503200-52506400	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr3:52503400-52506200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:52503400-52517200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr3:52503600-52507600	Weak transcription	Fetal Brain Male	brain
34	chr3:52504200-52517200	Strong transcription	Placenta Amnion	Placenta Amnion
35	chr3:52504200-52526600	Strong transcription	H9 Cell Line	embryonic stem cell
36	chr3:52504200-52526800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr3:52504200-52527400	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr3:52504200-52527400	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr3:52504200-52527600	Strong transcription	Dnd41	blood
40	chr3:52504200-52527800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:52504200-52528000	Strong transcription	Primary B cells from peripheral blood	blood
42	chr3:52504200-52528000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr3:52504200-52528600	Strong transcription	Brain Germinal Matrix	brain
44	chr3:52504400-52506400	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr3:52504400-52506800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr3:52504400-52508200	Strong transcription	NHLF	lung
47	chr3:52504400-52508400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr3:52504400-52517000	Strong transcription	GM12878-XiMat	blood
49	chr3:52504400-52517400	Strong transcription	NHEK	skin
50	chr3:52504400-52517600	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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