Variant report

Variant	rs72956638
Chromosome Location	chr2:99351464-99351465
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	EP300	chr2:99351189-99351885	HepG2	liver:	n/a	chr2:99351245-99351259 chr2:99351249-99351258 chr2:99351622-99351635 chr2:99351200-99351214
2	CCNT2	chr2:99351308-99351749	K562	blood:	n/a	chr2:99351739-99351748
3	MBD4	chr2:99351220-99351851	HepG2	liver:	n/a	n/a
4	NR2F2	chr2:99351399-99351719	K562	blood:	n/a	n/a
5	EP300	chr2:99351248-99351915	HepG2	liver:	n/a	chr2:99351249-99351258 chr2:99351622-99351635
6	POLR2A	chr2:99351340-99351636	K562	blood:	n/a	n/a
7	NR2F2	chr2:99351258-99351748	K562	blood:	n/a	n/a
8	TEAD4	chr2:99351197-99351765	K562	blood:	n/a	n/a
9	SP1	chr2:99351262-99351847	HepG2	liver:	n/a	chr2:99351739-99351753
10	TCF7L2	chr2:99351257-99351888	HepG2	liver:	n/a	chr2:99351637-99351651
11	MAFK	chr2:99351428-99351724	HepG2	liver:	n/a	n/a
12	NFIC	chr2:99351168-99351891	HepG2	liver:	n/a	n/a
13	FOXA1	chr2:99351215-99351899	HepG2	liver:	n/a	n/a
14	ATF1	chr2:99351376-99351732	K562	blood:	n/a	n/a
15	MYBL2	chr2:99351189-99351806	HepG2	liver:	n/a	n/a
16	RXRA	chr2:99351362-99351795	HepG2	liver:	n/a	n/a
17	TRIM28	chr2:99351241-99351703	K562	blood:	n/a	n/a
18	CEBPB	chr2:99351443-99351657	HepG2	liver:	n/a	n/a
19	NFIC	chr2:99351302-99351819	HepG2	liver:	n/a	n/a
20	MAX	chr2:99351171-99351811	HepG2	liver:	n/a	n/a
21	FOXA2	chr2:99351248-99351831	HepG2	liver:	n/a	n/a
22	TEAD4	chr2:99351121-99351890	HepG2	liver:	n/a	n/a
23	JUND	chr2:99351444-99351735	HepG2	liver:	n/a	n/a
24	STAT5A	chr2:99351262-99351783	K562	blood:	n/a	chr2:99351694-99351709 chr2:99351695-99351709 chr2:99351580-99351595 chr2:99351279-99351290
25	HMGN3	chr2:99351442-99351748	K562	blood:	n/a	n/a
26	RCOR1	chr2:99351256-99351821	K562	blood:	n/a	n/a
27	SMC3	chr2:99351319-99351749	HepG2	liver:	n/a	n/a
28	MAZ	chr2:99351451-99351755	HepG2	liver:	n/a	n/a
29	EP300	chr2:99351279-99351742	HepG2	liver:	n/a	chr2:99351622-99351635
30	PML	chr2:99351260-99351715	K562	blood:	n/a	n/a
31	RCOR1	chr2:99351274-99351764	HepG2	liver:	n/a	n/a
32	ARID3A	chr2:99351304-99351833	K562	blood:	n/a	n/a
33	RUNX3	chr2:99351270-99351661	GM12878	blood:	n/a	chr2:99351466-99351475 chr2:99351466-99351475
34	RCOR1	chr2:99351385-99351731	K562	blood:	n/a	n/a
35	JUND	chr2:99351353-99351758	HepG2	liver:	n/a	n/a
36	GABPA	chr2:99351339-99351718	K562	blood:	n/a	n/a
37	HDAC2	chr2:99351220-99351801	HepG2	liver:	n/a	chr2:99351257-99351271 chr2:99351633-99351647
38	JUND	chr2:99351408-99351839	HepG2	liver:	n/a	n/a
39	HDAC2	chr2:99351430-99351655	K562	blood:	n/a	chr2:99351633-99351647
40	PML	chr2:99351267-99351661	K562	blood:	n/a	n/a
41	HNF4A	chr2:99351254-99351809	HepG2	liver:	n/a	n/a
42	GATA1	chr2:99351224-99351795	PBDE	blood:	n/a	chr2:99351634-99351644 chr2:99351691-99351698 chr2:99351638-99351649 chr2:99351247-99351257
43	CEBPD	chr2:99351301-99351703	K562	blood:	n/a	n/a
44	ARID3A	chr2:99351261-99351842	HepG2	liver:	n/a	n/a
45	NR2F2	chr2:99351289-99351882	HepG2	liver:	n/a	n/a
46	CREB1	chr2:99351272-99351910	HepG2	liver:	n/a	n/a
47	POLR2A	chr2:99351296-99351685	K562	blood:	n/a	n/a
48	CEBPD	chr2:99351255-99351835	K562	blood:	n/a	n/a
49	MBD4	chr2:99351181-99351800	HepG2	liver:	n/a	n/a
50	GATA2	chr2:99351277-99351749	K562	blood:	n/a	chr2:99351634-99351644 chr2:99351691-99351698 chr2:99351638-99351649

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:99346676..99348606-chr2:99349694..99353065,3	MCF-7	breast:

Variant related genes	Relation type
MGAT4A	TF binding region
ENSG00000071073	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs56923186	1.00[AMR][1000 genomes]
rs58738020	1.00[AMR][1000 genomes]
rs58821307	1.00[AMR][1000 genomes]
rs59365702	1.00[AMR][1000 genomes]
rs60523550	1.00[AMR][1000 genomes]
rs60725966	1.00[AMR][1000 genomes]
rs60745907	1.00[AMR][1000 genomes]
rs61503115	1.00[AMR][1000 genomes]
rs72956620	0.95[AFR][1000 genomes]
rs72956659	1.00[AMR][1000 genomes]
rs72956663	1.00[AMR][1000 genomes]
rs72957625	1.00[AMR][1000 genomes]
rs72957633	1.00[AMR][1000 genomes]
rs72957643	1.00[AMR][1000 genomes]
rs72957654	1.00[AMR][1000 genomes]
rs72957656	1.00[AMR][1000 genomes]
rs72957660	1.00[AMR][1000 genomes]
rs72957672	1.00[AMR][1000 genomes]
rs72958630	1.00[AMR][1000 genomes]
rs72958634	1.00[AMR][1000 genomes]
rs72958636	1.00[AMR][1000 genomes]
rs72958646	1.00[AMR][1000 genomes]
rs72958649	1.00[AMR][1000 genomes]
rs72958653	1.00[AMR][1000 genomes]
rs72958659	1.00[AMR][1000 genomes]
rs72958661	1.00[AMR][1000 genomes]
rs72958666	1.00[AMR][1000 genomes]
rs72960709	1.00[AMR][1000 genomes]
rs73965241	1.00[AMR][1000 genomes]
rs73965242	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv535836	chr2:99329084-99353519	Active TSS Bivalent/Poised TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv535837	chr2:99329084-99358356	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv535838	chr2:99335416-99358356	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99348400-99352600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:99348400-99352600	Weak transcription	Small Intestine	intestine
3	chr2:99348400-99367000	Weak transcription	Esophagus	oesophagus
4	chr2:99348600-99353000	Weak transcription	NHEK	skin
5	chr2:99348600-99359200	Weak transcription	Aorta	Aorta
6	chr2:99348800-99351800	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr2:99348800-99352600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:99348800-99353000	Weak transcription	HMEC	breast
9	chr2:99348800-99360600	Weak transcription	Lung	lung
10	chr2:99349200-99357200	Enhancers	HepG2	liver
11	chr2:99349400-99352600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr2:99349400-99353800	Weak transcription	Pancreas	Pancrea
13	chr2:99349400-99355800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr2:99349800-99355200	Enhancers	Fetal Thymus	thymus
15	chr2:99350000-99351800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
16	chr2:99350200-99351600	Enhancers	Primary B cells from cord blood	blood
17	chr2:99350200-99351800	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr2:99350200-99351800	Enhancers	Duodenum Mucosa	Duodenum
19	chr2:99350200-99352200	Weak transcription	Placenta	Placenta
20	chr2:99350400-99351800	Enhancers	Primary B cells from peripheral blood	blood
21	chr2:99350400-99351800	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr2:99350400-99353200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr2:99350600-99351800	Flanking Active TSS	Primary T cells from cord blood	blood
24	chr2:99350600-99351800	Enhancers	Primary hematopoietic stem cells	blood
25	chr2:99350600-99351800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
26	chr2:99350600-99351800	Enhancers	Fetal Intestine Large	intestine
27	chr2:99350800-99351600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr2:99350800-99351600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
29	chr2:99350800-99351600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr2:99350800-99351600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
31	chr2:99350800-99351600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
32	chr2:99350800-99351600	Flanking Active TSS	Dnd41	blood
33	chr2:99350800-99351600	Enhancers	GM12878-XiMat	blood
34	chr2:99350800-99351800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
35	chr2:99350800-99351800	Enhancers	Fetal Intestine Small	intestine
36	chr2:99350800-99351800	Enhancers	Thymus	Thymus
37	chr2:99350800-99352800	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr2:99351000-99351800	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr2:99351200-99352400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr2:99351200-99355600	Enhancers	Primary T cells fromperipheralblood	blood
41	chr2:99351400-99351600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
42	chr2:99351400-99351600	Enhancers	Brain Anterior Caudate	brain
43	chr2:99351400-99351600	Enhancers	Psoas Muscle	Psoas
44	chr2:99351400-99351600	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr2:99351400-99351600	Enhancers	Stomach Mucosa	stomach
46	chr2:99351400-99351600	Enhancers	Spleen	Spleen
47	chr2:99351400-99351800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
48	chr2:99351400-99352600	Enhancers	Monocytes-CD14+_RO01746	blood
49	chr2:99351400-99352800	Weak transcription	HUVEC	blood vessel
50	chr2:99351400-99355000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

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