Variant report

Variant	rs55813111
Chromosome Location	chr2:47270504-47270505
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	ELK1	chr2:47270359-47271043	Hela-S3	cervix:	n/a	n/a
2	MAX	chr2:47269972-47271293	SK-N-SH	brain:	n/a	chr2:47271221-47271231
3	CTCF	chr2:47270500-47270650	HepG2	liver:	n/a	n/a
4	PBX3	chr2:47270025-47271248	SK-N-SH	brain:	n/a	n/a
5	MAX	chr2:47269965-47271591	A549	lung:	n/a	chr2:47271221-47271231
6	MAX	chr2:47270409-47271287	ECC-1	luminal epithelium:	n/a	chr2:47271221-47271231
7	EP300	chr2:47270032-47271419	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr2:47270084-47271237	HUVEC	blood vessel:	n/a	n/a
9	TEAD4	chr2:47270392-47271429	A549	lung:	n/a	chr2:47270938-47270947
10	CTCF	chr2:47270400-47270550	AG04450	lung:	n/a	n/a
11	CTCF	chr2:47270380-47270530	AG04450	lung:	n/a	n/a
12	USF1	chr2:47270479-47270851	A549	lung:	n/a	chr2:47270626-47270637
13	GATA3	chr2:47270101-47271303	SK-N-SH	brain:	n/a	chr2:47270402-47270410 chr2:47270671-47270681
14	RAD21	chr2:47270282-47271176	A549	lung:	n/a	chr2:47271117-47271131
15	RAD21	chr2:47270119-47271184	SK-N-SH_RA	brain:	n/a	chr2:47271117-47271131
16	USF2	chr2:47270311-47271084	HepG2	liver:	n/a	chr2:47270626-47270637
17	CTCF	chr2:47270460-47270610	HCFaa	heart:	n/a	n/a
18	USF1	chr2:47270436-47270784	A549	lung:	n/a	chr2:47270626-47270637
19	RAD21	chr2:47270351-47270657	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr2:47270340-47271099	HUVEC	blood vessel:	n/a	n/a
21	USF1	chr2:47270420-47270776	SK-N-SH_RA	brain:	n/a	chr2:47270626-47270637
22	RAD21	chr2:47270298-47270738	HepG2	liver:	n/a	n/a
23	RAD21	chr2:47270229-47270622	SK-N-SH_RA	brain:	n/a	n/a
24	POLR2A	chr2:47270382-47270981	HepG2	liver:	n/a	n/a
25	FOS	chr2:47270312-47271272	HUVEC	blood vessel:	n/a	chr2:47270928-47270935 chr2:47271077-47271086
26	TEAD4	chr2:47270035-47271376	SK-N-SH	brain:	n/a	chr2:47270938-47270947
27	POLR2A	chr2:47269825-47271250	SK-N-SH	brain:	n/a	n/a
28	POLR2A	chr2:47270500-47271028	MCF10A-Er-Src	breast:	n/a	n/a
29	POLR2A	chr2:47270442-47271150	Hela-S3	cervix:	n/a	n/a
30	CTCF	chr2:47270449-47270558	NHEK	skin:	n/a	n/a
31	JUND	chr2:47270088-47271320	SK-N-SH	brain:	n/a	chr2:47270928-47270935 chr2:47270104-47270115 chr2:47271077-47271086
32	POLR2A	chr2:47270496-47271181	HCT-116	colon:	n/a	n/a
33	SP1	chr2:47270192-47271211	A549	lung:	n/a	n/a
34	POLR2A	chr2:47270203-47271017	Hela-S3	cervix:	n/a	n/a
35	TCF12	chr2:47269774-47271711	SK-N-SH	brain:	n/a	chr2:47270093-47270103 chr2:47270353-47270362 chr2:47271263-47271273 chr2:47271628-47271635
36	CTCF	chr2:47270380-47270530	HMF	breast:	n/a	n/a
37	TEAD4	chr2:47270249-47271241	SK-N-SH	brain:	n/a	chr2:47270938-47270947
38	TAF1	chr2:47270233-47271165	SK-N-SH	brain:	n/a	n/a
39	CTCF	chr2:47270485-47270520	Kidney_OC	kidney:	n/a	n/a
40	JUND	chr2:47270040-47271351	SK-N-SH	brain:	n/a	chr2:47270928-47270935 chr2:47270104-47270115 chr2:47271077-47271086
41	SMC3	chr2:47270275-47271353	Hela-S3	cervix:	n/a	chr2:47271244-47271258
42	CTCF	chr2:47270500-47270650	AoAF	blood vessel:	n/a	n/a
43	RAD21	chr2:47270420-47270554	K562	blood:	n/a	n/a
44	POLR2A	chr2:47270307-47271086	A549	lung:	n/a	n/a
45	CTCF	chr2:47270440-47270590	HRPEpiC	eye:	n/a	n/a
46	CTCF	chr2:47270471-47270523	Spleen_OC	spleen:	n/a	n/a
47	POLR2A	chr2:47270208-47270905	ProgFib	skin:	n/a	n/a
48	NR2F2	chr2:47270260-47271188	MCF-7	breast:	n/a	n/a
49	USF1	chr2:47270170-47271145	SK-N-SH	brain:	n/a	chr2:47270626-47270637
50	EP300	chr2:47270167-47271236	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:47250659..47252384-chr2:47268724..47270646,2	MCF-7	breast:
2	chr2:47269303..47271501-chr2:47388884..47391156,2	MCF-7	breast:
3	chr2:47265695..47269045-chr2:47269203..47272873,4	K562	blood:
4	chr2:47265110..47267582-chr2:47269199..47272729,4	MCF-7	breast:
5	chr2:47269231..47272270-chr2:47291974..47297806,6	MCF-7	breast:
6	chr2:47269929..47271605-chr2:47280947..47283889,2	MCF-7	breast:
7	chr2:47269944..47272346-chr2:47548303..47550473,2	MCF-7	breast:
8	chr2:47270183..47272803-chr2:47401195..47403585,3	K562	blood:

Variant related genes	Relation type
ENSG00000233845	TF binding region
TTC7A	TF binding region
ENSG00000225187	Chromatin interaction
ENSG00000233845	Chromatin interaction
ENSG00000143933	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12373629	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13398062	1.00[ASN][1000 genomes]
rs28490098	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55813407	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55829028	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55855730	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55920732	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6729896	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72808511	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72808512	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72808515	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72808516	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72808520	0.96[ASN][1000 genomes]
rs7563297	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
5	nsv524970	chr2:47162739-47302095	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1000377	chr2:47189386-47344029	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv525197	chr2:47210747-47297973	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv984532	chr2:47237908-47270533	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv528091	chr2:47249239-47273732	Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 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	chr2:47230200-47302800	Strong transcription	Dnd41	blood
2	chr2:47234400-47283600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr2:47236000-47278600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr2:47246000-47283800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr2:47246800-47281600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr2:47252000-47283400	Strong transcription	Thymus	Thymus
7	chr2:47255600-47273400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr2:47257000-47277000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr2:47258400-47282600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr2:47259600-47295000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr2:47261800-47273600	Weak transcription	Fetal Brain Female	brain
12	chr2:47262000-47283400	Weak transcription	Fetal Brain Male	brain
13	chr2:47262000-47283600	Weak transcription	Small Intestine	intestine
14	chr2:47263000-47283200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr2:47263400-47283200	Weak transcription	Fetal Kidney	kidney
16	chr2:47265000-47273200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:47265000-47273400	Weak transcription	K562	blood
18	chr2:47266000-47271600	Enhancers	Duodenum Smooth Muscle	Duodenum
19	chr2:47266200-47280800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr2:47266400-47271000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr2:47266400-47280200	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr2:47266400-47283000	Strong transcription	Primary T cells from cord blood	blood
23	chr2:47266600-47272400	Enhancers	Brain Substantia Nigra	brain
24	chr2:47266600-47272800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr2:47266600-47282600	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr2:47266800-47272600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:47266800-47282800	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr2:47267200-47272200	Enhancers	Brain Hippocampus Middle	brain
29	chr2:47267200-47281400	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr2:47267200-47282800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr2:47267400-47271200	Enhancers	Fetal Muscle Trunk	muscle
32	chr2:47267400-47271400	Genic enhancers	Fetal Stomach	stomach
33	chr2:47267400-47273200	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr2:47267400-47282600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr2:47267800-47272600	Enhancers	Fetal Muscle Leg	muscle
36	chr2:47268000-47271200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr2:47268200-47272000	Weak transcription	Gastric	stomach
38	chr2:47268200-47273000	Enhancers	Brain Anterior Caudate	brain
39	chr2:47268400-47270800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr2:47268400-47271200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr2:47268400-47271400	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr2:47268600-47270600	Weak transcription	Fetal Intestine Large	intestine
43	chr2:47268600-47271000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr2:47268600-47271800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr2:47268600-47273000	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr2:47268600-47274000	Enhancers	Brain Cingulate Gyrus	brain
47	chr2:47268600-47282000	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr2:47269000-47270800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr2:47269000-47271000	Enhancers	HUES48 Cell Line	embryonic stem cell
50	chr2:47269000-47271400	Enhancers	HUES64 Cell Line	embryonic stem cell

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