Variant report

Variant	rs72982505
Chromosome Location	chr3:140974894-140974895
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	CTCF	chr3:140974860-140975010	GM12869	blood:	n/a	n/a
2	RAD21	chr3:140974678-140975198	A549	lung:	n/a	chr3:140974927-140974941 chr3:140975086-140975098
3	MAX	chr3:140974789-140975108	K562	blood:	n/a	n/a
4	RAD21	chr3:140974759-140975200	HepG2	liver:	n/a	chr3:140974927-140974941 chr3:140975086-140975098
5	CTCF	chr3:140974742-140975100	HepG2	liver:	n/a	n/a
6	CTCF	chr3:140974833-140975113	K562	blood:	n/a	n/a
7	CTCF	chr3:140974746-140975053	T-47D	breast:	n/a	n/a
8	MAX	chr3:140974725-140975054	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr3:140974860-140975010	SK-N-SH_RA	brain:	n/a	n/a
10	CTCF	chr3:140974880-140975030	AG10803	skin:	n/a	n/a
11	TBL1XR1	chr3:140974875-140975217	K562	blood:	n/a	n/a
12	CHD2	chr3:140974842-140974995	HepG2	liver:	n/a	n/a
13	ELF1	chr3:140974791-140975164	K562	blood:	n/a	n/a
14	CTCF	chr3:140974713-140975156	A549	lung:	n/a	n/a
15	CTCF	chr3:140974880-140975030	HCFaa	heart:	n/a	n/a
16	CTCF	chr3:140974880-140975030	GM12873	blood:	n/a	n/a
17	UBTF	chr3:140974835-140975132	K562	blood:	n/a	n/a
18	RAD21	chr3:140974837-140975045	K562	blood:	n/a	chr3:140974927-140974941
19	RAD21	chr3:140974753-140975098	SK-N-SH_RA	brain:	n/a	chr3:140974927-140974941 chr3:140975086-140975098
20	CTCF	chr3:140974868-140975087	GM12878	blood:	n/a	n/a
21	SMC3	chr3:140974866-140975066	GM12878	blood:	n/a	n/a
22	RAD21	chr3:140974669-140975178	SK-N-SH	brain:	n/a	chr3:140974927-140974941 chr3:140975086-140975098
23	CTCF	chr3:140974819-140975076	MCF-7	breast:	n/a	n/a
24	CTCF	chr3:140974840-140974990	GM12875	blood:	n/a	n/a
25	ARID3A	chr3:140974877-140975077	HepG2	liver:	n/a	n/a
26	MAX	chr3:140974733-140975121	K562	blood:	n/a	n/a
27	MAZ	chr3:140974846-140975013	HepG2	liver:	n/a	n/a
28	CTCF	chr3:140974880-140975030	HPF	lung:	n/a	n/a
29	CTCF	chr3:140974859-140975047	GM10248	blood:	n/a	n/a
30	CTCF	chr3:140974645-140975142	K562	blood:	n/a	n/a
31	CTCF	chr3:140974857-140975088	MCF-7	breast:	n/a	n/a
32	RAD21	chr3:140974811-140975149	K562	blood:	n/a	chr3:140974927-140974941 chr3:140975086-140975098
33	CTCF	chr3:140974777-140975166	H1-hESC	embryonic stem cell:	n/a	n/a
34	RAD21	chr3:140974692-140975161	H1-hESC	embryonic stem cell:	n/a	chr3:140974927-140974941 chr3:140975086-140975098
35	CTCF	chr3:140974861-140975068	A549	lung:	n/a	n/a
36	CTCF	chr3:140974880-140975030	GM12875	blood:	n/a	n/a
37	CTCF	chr3:140974840-140975036	SK-N-SH_RA	brain:	n/a	n/a
38	CTCF	chr3:140974880-140975030	WI-38	lung:	n/a	n/a
39	CTCF	chr3:140974818-140975114	IMR90	lung:	n/a	n/a
40	CTCF	chr3:140974732-140975107	K562	blood:	n/a	n/a
41	CTCF	chr3:140974730-140975127	H1-hESC	embryonic stem cell:	n/a	n/a
42	CTCF	chr3:140974882-140975056	GM19238	blood:	n/a	n/a
43	CTCF	chr3:140974890-140975076	Pancreas_OC	pancreas:	n/a	n/a
44	RAD21	chr3:140974684-140975118	SK-N-SH_RA	brain:	n/a	chr3:140974927-140974941 chr3:140975086-140975098
45	RAD21	chr3:140974726-140975271	MCF-7	breast:	n/a	chr3:140974927-140974941 chr3:140975086-140975098
46	CTCF	chr3:140974829-140975088	Gliobla	brain:	n/a	n/a
47	CTCF	chr3:140974860-140975104	LNCaP	prostate:	n/a	n/a
48	CTCF	chr3:140974626-140975308	SK-N-SH	brain:	n/a	n/a
49	EP300	chr3:140974877-140975157	K562	blood:	n/a	n/a
50	RAD21	chr3:140974757-140975145	H1-hESC	embryonic stem cell:	n/a	chr3:140974927-140974941 chr3:140975086-140975098

No.	Distal block	Cell Line	Cell type
1	chr3:140965187..140967978-chr3:140974233..140977075,2	MCF-7	breast:
2	chr3:140950121..140951283-chr3:140974013..140975399,11	MCF-7	breast:
3	chr3:140950250..140950957-chr3:140974321..140975028,2	K562	blood:
4	chr3:140718858..140719528-chr3:140974880..140975512,2	K562	blood:
5	chr3:140973529..140975169-chr3:141030843..141032626,2	K562	blood:
6	chr3:140954123..140955100-chr3:140974846..140975403,3	K562	blood:
7	chr3:140946870..140947785-chr3:140974833..140975602,3	MCF-7	breast:
8	chr3:140968757..140971307-chr3:140972187..140974906,2	MCF-7	breast:
9	chr3:140910927..140911916-chr3:140974455..140975357,4	MCF-7	breast:
10	chr3:140967710..140969385-chr3:140973413..140974943,2	K562	blood:
11	chr3:140950441..140951108-chr3:140974772..140975328,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000241400	TF binding region
ENSG00000155893	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs16851210	1.00[EUR][1000 genomes]
rs16851215	1.00[EUR][1000 genomes]
rs16851264	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61539616	1.00[EUR][1000 genomes]
rs61710141	1.00[EUR][1000 genomes]
rs6773280	1.00[EUR][1000 genomes]
rs6779202	1.00[EUR][1000 genomes]
rs72982504	1.00[EUR][1000 genomes]
rs72982506	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72982513	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72982515	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72982516	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72982519	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72982581	0.81[AFR][1000 genomes]
rs72994972	1.00[EUR][1000 genomes]
rs73869568	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460870	chr3:140938546-141005574	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv591892	chr3:140938546-141005574	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv877551	chr3:140970556-141029860	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140951600-140979000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:140955200-140980600	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr3:140955400-140985800	Weak transcription	Duodenum Mucosa	Duodenum
4	chr3:140957400-141001000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:140959200-140998400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr3:140960000-140980000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr3:140961000-140978800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:140961200-140985800	Weak transcription	Adipose Nuclei	Adipose
9	chr3:140961200-141012600	Weak transcription	Aorta	Aorta
10	chr3:140961400-140983200	Weak transcription	Stomach Smooth Muscle	stomach
11	chr3:140962000-140985800	Weak transcription	Brain Anterior Caudate	brain
12	chr3:140962400-140977000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:140962400-140979200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:140962600-140975000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr3:140962600-140978800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:140962600-140979600	Weak transcription	Fetal Intestine Large	intestine
17	chr3:140962600-140980600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:140963400-140982800	Weak transcription	Brain Germinal Matrix	brain
19	chr3:140963600-140978800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr3:140964800-140978000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:140966000-140990200	Weak transcription	Psoas Muscle	Psoas
22	chr3:140966200-140979600	Weak transcription	Pancreas	Pancrea
23	chr3:140968000-140976600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:140968200-140979000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr3:140968200-140990000	Weak transcription	Gastric	stomach
26	chr3:140968400-140982800	Weak transcription	Fetal Lung	lung
27	chr3:140971000-140979000	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr3:140971600-140976600	Enhancers	Fetal Heart	heart
29	chr3:140971600-140976800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:140971800-140977000	Enhancers	Thymus	Thymus
31	chr3:140972000-140979000	Weak transcription	Fetal Intestine Small	intestine
32	chr3:140972200-140979000	Weak transcription	Fetal Stomach	stomach
33	chr3:140972400-140975200	Weak transcription	Primary T cells from cord blood	blood
34	chr3:140973200-140976200	Enhancers	Fetal Muscle Leg	muscle
35	chr3:140973200-140979000	Enhancers	Fetal Thymus	thymus
36	chr3:140973600-140977000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr3:140974000-140975800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr3:140974000-140976400	Enhancers	Fetal Brain Male	brain
39	chr3:140974200-140975000	Enhancers	Brain Angular Gyrus	brain
40	chr3:140974200-140975000	Enhancers	Brain Cingulate Gyrus	brain
41	chr3:140974200-140975000	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr3:140974200-140975000	Enhancers	Brain Substantia Nigra	brain
43	chr3:140974200-140975200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
44	chr3:140974200-140975400	Enhancers	Right Ventricle	heart
45	chr3:140974200-140975400	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr3:140974200-140975400	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr3:140974200-140975800	Enhancers	Fetal Muscle Trunk	muscle
48	chr3:140974200-140975800	Enhancers	HSMMtube	muscle
49	chr3:140974400-140975000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr3:140974400-140975000	Enhancers	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links