Variant report

Variant	rs73049331
Chromosome Location	chr7:2799911-2799912
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	USF1	chr7:2799473-2799978	A549	lung:	n/a	chr7:2799603-2799624
2	BHLHE40	chr7:2799673-2799981	A549	lung:	n/a	n/a
3	TCF7L2	chr7:2799411-2800583	PANC-1	pancreas:	n/a	chr7:2800034-2800048 chr7:2799527-2799534
4	CTCF	chr7:2799836-2800582	K562	blood:	n/a	chr7:2799932-2799940
5	CTCF	chr7:2799880-2800030	HCFaa	heart:	n/a	chr7:2799932-2799940
6	CTCF	chr7:2799910-2799955	NHEK	skin:	n/a	chr7:2799932-2799940
7	CTCF	chr7:2799859-2799912	MCF-7	breast:	n/a	n/a
8	CTCF	chr7:2799820-2799970	HMF	breast:	n/a	chr7:2799932-2799940
9	CTCF	chr7:2799840-2799990	NHEK	skin:	n/a	chr7:2799932-2799940
10	POLR2A	chr7:2799807-2799979	MCF-7	breast:	n/a	n/a
11	MAX	chr7:2799620-2800540	Hela-S3	cervix:	n/a	chr7:2799768-2799777
12	MAX	chr7:2799408-2800718	A549	lung:	n/a	chr7:2799609-2799618 chr7:2799768-2799777
13	MAX	chr7:2799646-2800546	Hela-S3	cervix:	n/a	chr7:2799768-2799777
14	CTCF	chr7:2799091-2801195	SK-N-SH	brain:	n/a	chr7:2799932-2799940 chr7:2800947-2800960 chr7:2800945-2800963 chr7:2799554-2799567
15	TCF7L2	chr7:2799542-2800460	Hela-S3	cervix:	n/a	chr7:2800034-2800048
16	CTCF	chr7:2799800-2799950	Caco-2	colon:	n/a	chr7:2799932-2799940
17	RUNX3	chr7:2799880-2800516	GM12878	blood:	n/a	n/a
18	CTCF	chr7:2799553-2801013	A549	lung:	n/a	chr7:2799932-2799940 chr7:2800947-2800960 chr7:2800945-2800963 chr7:2799554-2799567
19	POLR2A	chr7:2799697-2800079	H1-hESC	embryonic stem cell:	n/a	n/a
20	CTCF	chr7:2799900-2800050	GM12872	blood:	n/a	chr7:2799932-2799940
21	BHLHE40	chr7:2799641-2799911	HepG2	liver:	n/a	n/a
22	MXI1	chr7:2799656-2800020	Hela-S3	cervix:	n/a	n/a
23	MAX	chr7:2799537-2800659	A549	lung:	n/a	chr7:2799609-2799618 chr7:2799768-2799777
24	USF2	chr7:2799532-2800413	Hela-S3	cervix:	n/a	chr7:2799603-2799624
25	MAX	chr7:2799445-2800054	K562	blood:	n/a	chr7:2799609-2799618 chr7:2799768-2799777
26	SP1	chr7:2799744-2800600	A549	lung:	n/a	chr7:2800534-2800548
27	BHLHE40	chr7:2799594-2800567	K562	blood:	n/a	chr7:2799603-2799624
28	TCF7L2	chr7:2799869-2800216	MCF-7	breast:	n/a	chr7:2800034-2800048
29	USF1	chr7:2799416-2799988	A549	lung:	n/a	chr7:2799603-2799624
30	POLR2A	chr7:2799879-2800644	K562	blood:	n/a	n/a
31	MAX	chr7:2799681-2799936	A549	lung:	n/a	chr7:2799768-2799777
32	CTCF	chr7:2799840-2799990	GM06990	blood:	n/a	chr7:2799932-2799940
33	TCF12	chr7:2799392-2800672	A549	lung:	n/a	chr7:2800573-2800583 chr7:2799557-2799567 chr7:2799515-2799522
34	USF1	chr7:2799605-2799948	A549	lung:	n/a	n/a
35	USF1	chr7:2799537-2799955	A549	lung:	n/a	chr7:2799603-2799624
36	RAD21	chr7:2799243-2801814	SK-N-SH	brain:	n/a	chr7:2799554-2799564 chr7:2799556-2799570
37	SMC3	chr7:2799728-2800023	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr7:2799824-2799936	HUVEC	blood vessel:	n/a	n/a
39	POLR2A	chr7:2799734-2800241	MCF-7	breast:	n/a	n/a
40	POLR2A	chr7:2799566-2800824	PANC-1	pancreas:	n/a	n/a
41	MYC	chr7:2799770-2799984	MCF-7	breast:	n/a	n/a
42	CHD2	chr7:2799868-2800025	Hela-S3	cervix:	n/a	n/a
43	MAX	chr7:2799707-2799914	K562	blood:	n/a	chr7:2799768-2799777
44	CEBPB	chr7:2799706-2800423	Hela-S3	cervix:	n/a	chr7:2800243-2800255
45	CTCF	chr7:2799860-2800010	AG09319	gingival:	n/a	chr7:2799932-2799940
46	JUND	chr7:2799787-2799941	K562	blood:	n/a	n/a
47	SMARCB1	chr7:2799703-2800890	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:2726208..2729496-chr7:2795829..2800431,6	MCF-7	breast:
2	chr7:2797400..2800902-chr7:2803018..2805102,3	MCF-7	breast:

Variant related genes	Relation type
AMZ1	TF binding region
ENSG00000174945	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11761804	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11764225	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11765492	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11765726	0.81[AMR][1000 genomes]
rs11769532	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11772508	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11971014	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12540539	0.82[AMR][1000 genomes]
rs17132594	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17132624	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17132665	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17132744	0.81[AMR][1000 genomes]
rs17241904	0.82[AMR][1000 genomes]
rs17300022	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55726557	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55767077	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55776032	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55832916	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56007918	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56208415	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56356906	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56399783	0.86[EUR][1000 genomes]
rs6461600	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6964740	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6967664	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73033403	0.86[AMR][1000 genomes]
rs73033407	0.84[AMR][1000 genomes]
rs73033408	0.84[AMR][1000 genomes]
rs73047343	0.82[EUR][1000 genomes]
rs73047355	0.80[EUR][1000 genomes]
rs73047368	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73047387	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73047393	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73049305	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73049327	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73049341	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73049362	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73049380	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73051415	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73051469	0.86[AMR][1000 genomes]
rs757788	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7803944	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7804264	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7811164	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9770108	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029250	chr7:2722737-2881021	Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv538652	chr7:2722737-2881021	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1024023	chr7:2726210-2829581	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv538653	chr7:2726210-2829581	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv1015700	chr7:2753965-2945848	Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv1032282	chr7:2789555-2820774	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1022612	chr7:2789555-3019200	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:2775400-2801200	Weak transcription	Primary T cells from cord blood	blood
2	chr7:2789200-2831600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr7:2790000-2830400	Weak transcription	Aorta	Aorta
4	chr7:2791200-2803400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr7:2791400-2800200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr7:2796400-2800600	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr7:2796400-2801000	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr7:2796400-2801600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr7:2796400-2803200	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr7:2796400-2804000	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr7:2796800-2801000	Enhancers	Fetal Intestine Large	intestine
12	chr7:2796800-2802000	Enhancers	Adipose Nuclei	Adipose
13	chr7:2796800-2803600	Weak transcription	Primary B cells from cord blood	blood
14	chr7:2796800-2804400	Enhancers	Fetal Muscle Leg	muscle
15	chr7:2797000-2800200	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr7:2797000-2800800	Enhancers	Primary T cells fromperipheralblood	blood
17	chr7:2797000-2800800	Enhancers	Primary hematopoietic stem cells	blood
18	chr7:2797000-2801000	Enhancers	Brain Germinal Matrix	brain
19	chr7:2797000-2801000	Enhancers	Fetal Thymus	thymus
20	chr7:2797000-2801800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr7:2797000-2803200	Enhancers	Right Ventricle	heart
22	chr7:2797000-2803800	Enhancers	Brain Cingulate Gyrus	brain
23	chr7:2797000-2805400	Enhancers	Placenta	Placenta
24	chr7:2797200-2801000	Enhancers	Small Intestine	intestine
25	chr7:2797400-2801200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr7:2797600-2800800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr7:2797600-2831200	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr7:2797800-2800400	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr7:2797800-2801000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr7:2798000-2800000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr7:2798000-2800200	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr7:2798000-2800200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr7:2798000-2801200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr7:2798000-2801400	Enhancers	Psoas Muscle	Psoas
35	chr7:2798000-2803600	Enhancers	Placenta Amnion	Placenta Amnion
36	chr7:2798000-2827400	Weak transcription	Thymus	Thymus
37	chr7:2798200-2800000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr7:2798200-2800000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr7:2798200-2800000	Weak transcription	Fetal Kidney	kidney
40	chr7:2798200-2800000	Enhancers	HepG2	liver
41	chr7:2798200-2800200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr7:2798200-2800200	Enhancers	Brain Hippocampus Middle	brain
43	chr7:2798200-2800600	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr7:2798200-2803200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr7:2798400-2800000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr7:2798400-2800000	Enhancers	Fetal Intestine Small	intestine
47	chr7:2798400-2800200	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr7:2798400-2800400	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr7:2798400-2800600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr7:2798400-2802000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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