Variant report

Variant	rs55957515
Chromosome Location	chr5:14663879-14663880
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	STAT5A	chr5:14663750-14664778	GM12878	blood:	n/a	chr5:14664526-14664533 chr5:14664590-14664602 chr5:14664532-14664544
2	SMARCC1	chr5:14663874-14665749	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr5:14663716-14665614	GM19099	blood:	n/a	n/a
4	MAX	chr5:14663814-14665184	HepG2	liver:	n/a	n/a
5	MYC	chr5:14663850-14665135	K562	blood:	n/a	n/a
6	POU2F2	chr5:14663861-14665039	GM12878	blood:	n/a	n/a
7	SRF	chr5:14663773-14664025	GM12878	blood:	n/a	n/a
8	POLR2A	chr5:14663644-14665544	GM12892	blood:	n/a	n/a
9	E2F6	chr5:14663861-14665118	H1-hESC	embryonic stem cell:	n/a	chr5:14664571-14664582 chr5:14664572-14664584 chr5:14664573-14664580 chr5:14664716-14664725 chr5:14664682-14664692 chr5:14664573-14664580 chr5:14664573-14664580
10	TCF12	chr5:14663789-14665444	A549	lung:	n/a	chr5:14664751-14664758
11	MXI1	chr5:14663874-14666710	GM12878	blood:	n/a	n/a
12	BCLAF1	chr5:14663727-14665699	GM12878	blood:	n/a	chr5:14664655-14664668 chr5:14664626-14664639 chr5:14664393-14664402 chr5:14664622-14664635
13	USF2	chr5:14663860-14664936	GM12878	blood:	n/a	chr5:14664652-14664668
14	RELA	chr5:14663789-14665721	GM18951	blood:	n/a	chr5:14664433-14664442 chr5:14664433-14664442
15	RELA	chr5:14663792-14665037	GM15510	blood:	n/a	chr5:14664433-14664442 chr5:14664433-14664442
16	NFATC1	chr5:14663712-14664792	GM12878	blood:	n/a	n/a
17	POLR2A	chr5:14663709-14664993	GM12891	blood:	n/a	n/a
18	POLR2A	chr5:14661991-14665007	K562	blood:	n/a	n/a
19	POLR2A	chr5:14663831-14665668	GM19193	blood:	n/a	n/a
20	PML	chr5:14663275-14665759	GM12878	blood:	n/a	n/a
21	ATF2	chr5:14663624-14664414	GM12878	blood:	n/a	n/a
22	POLR2A	chr5:14663820-14665209	U87	brain:	n/a	n/a
23	SETDB1	chr5:14663864-14664993	U2OS	brain:	n/a	chr5:14664716-14664725
24	HCFC1	chr5:14663672-14668468	Hela-S3	cervix:	n/a	n/a
25	NFIC	chr5:14663547-14664772	GM12878	blood:	n/a	n/a
26	POLR2A	chr5:14663829-14665047	GM12892	blood:	n/a	n/a
27	MAX	chr5:14663875-14665139	ECC-1	luminal epithelium:	n/a	n/a
28	MXI1	chr5:14663713-14665734	IMR90	lung:	n/a	n/a
29	FOXM1	chr5:14663761-14664980	GM12878	blood:	n/a	n/a
30	POLR2A	chr5:14663856-14665611	GM15510	blood:	n/a	n/a
31	MAX	chr5:14663814-14665763	A549	lung:	n/a	n/a
32	POLR2A	chr5:14663129-14665683	GM12878	blood:	n/a	n/a
33	BCLAF1	chr5:14663776-14665079	GM12878	blood:	n/a	chr5:14664655-14664668 chr5:14664626-14664639 chr5:14664393-14664402 chr5:14664622-14664635
34	MAX	chr5:14663874-14665107	SK-N-SH	brain:	n/a	n/a
35	RUNX3	chr5:14663734-14665046	GM12878	blood:	n/a	n/a
36	POLR2A	chr5:14663809-14665640	Raji	blood:	n/a	n/a
37	CHD1	chr5:14663829-14665056	GM12878	blood:	n/a	n/a
38	RELA	chr5:14663811-14665003	GM10847	blood:	n/a	chr5:14664433-14664442 chr5:14664433-14664442
39	POLR2A	chr5:14663752-14665106	GM12891	blood:	n/a	n/a
40	POLR2A	chr5:14663845-14665724	PBDE	blood:	n/a	n/a
41	RELA	chr5:14663800-14664942	GM19099	blood:	n/a	chr5:14664433-14664442 chr5:14664433-14664442
42	FOXM1	chr5:14663718-14665025	GM12878	blood:	n/a	n/a
43	POLR2A	chr5:14663694-14665059	GM12892	blood:	n/a	n/a
44	POLR2A	chr5:14663809-14665667	K562	blood:	n/a	n/a
45	HA-E2F1	chr5:14663839-14665694	MCF-7	breast:	n/a	chr5:14664572-14664584 chr5:14664573-14664580 chr5:14664716-14664725 chr5:14664682-14664692 chr5:14664573-14664580 chr5:14664573-14664580 chr5:14665460-14665470
46	POLR2A	chr5:14663726-14665639	GM18505	blood:	n/a	n/a
47	MAZ	chr5:14663804-14665971	IMR90	lung:	n/a	n/a
48	POLR2A	chr5:14663835-14665321	GM12878	blood:	n/a	n/a
49	BRCA1	chr5:14663757-14664910	Hela-S3	cervix:	n/a	n/a
50	MTA3	chr5:14663780-14664720	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:14497930..14500445-chr5:14662848..14665215,2	MCF-7	breast:
2	chr5:14663431..14670152-chr5:14672054..14680588,17	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ANKH-1	chr5:14663208-14664704	NONHSAT100548

Variant related genes	Relation type
FAM105B	TF binding region
ENSG00000038382	Chromatin interaction
ENSG00000154124	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11952550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11953822	1.00[AMR][1000 genomes]
rs11956097	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16903651	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55714227	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56044433	1.00[AMR][1000 genomes]
rs56155042	1.00[AMR][1000 genomes]
rs56297478	1.00[AMR][1000 genomes]
rs56350972	1.00[AMR][1000 genomes]
rs60753214	0.83[AMR][1000 genomes]
rs73749521	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73749524	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73749525	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73749526	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73749585	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73749586	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73749593	1.00[AMR][1000 genomes]
rs73749595	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73749596	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73752121	0.83[AMR][1000 genomes]
rs73752126	1.00[AMR][1000 genomes]
rs73752131	1.00[AMR][1000 genomes]
rs73752132	1.00[AMR][1000 genomes]
rs73752133	1.00[AMR][1000 genomes]
rs73752135	1.00[AMR][1000 genomes]
rs73752138	1.00[AMR][1000 genomes]
rs73752139	1.00[AMR][1000 genomes]
rs73752140	1.00[AMR][1000 genomes]
rs7710316	0.83[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	nsv1026914	chr5:14237782-14751588	Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active 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
2	nsv1018187	chr5:14385164-15127103	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv830211	chr5:14474675-14675776	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1032951	chr5:14529579-14667342	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv597254	chr5:14661675-14664951	Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14662800-14664200	Flanking Active TSS	NHEK	skin
2	chr5:14663200-14664200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr5:14663200-14664400	Flanking Active TSS	Dnd41	blood
4	chr5:14663400-14664000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr5:14663400-14664000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr5:14663400-14664000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr5:14663400-14664000	Flanking Active TSS	Duodenum Mucosa	Duodenum
8	chr5:14663400-14664000	Flanking Active TSS	Stomach Smooth Muscle	stomach
9	chr5:14663400-14664200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr5:14663400-14664200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
11	chr5:14663400-14664200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
12	chr5:14663400-14664200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr5:14663400-14664200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
14	chr5:14663400-14664400	Flanking Active TSS	Osteobl	bone
15	chr5:14663400-14665600	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr5:14663400-14665800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr5:14663400-14665800	Active TSS	A549	lung
18	chr5:14663600-14664000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr5:14663600-14664000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr5:14663600-14664000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
21	chr5:14663600-14664000	Flanking Active TSS	Fetal Intestine Large	intestine
22	chr5:14663600-14664000	Flanking Active TSS	Fetal Intestine Small	intestine
23	chr5:14663600-14664000	Flanking Active TSS	HepG2	liver
24	chr5:14663600-14664200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
25	chr5:14663600-14664200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
26	chr5:14663600-14664200	Flanking Active TSS	Primary T cells from cord blood	blood
27	chr5:14663600-14664200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
28	chr5:14663600-14664200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
29	chr5:14663600-14664200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr5:14663600-14664200	Flanking Active TSS	Brain Angular Gyrus	brain
31	chr5:14663600-14664200	Flanking Active TSS	Brain Germinal Matrix	brain
32	chr5:14663600-14664200	Flanking Active TSS	Fetal Brain Female	brain
33	chr5:14663600-14664200	Flanking Active TSS	Fetal Thymus	thymus
34	chr5:14663600-14664200	Flanking Active TSS	K562	blood
35	chr5:14663600-14664400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
36	chr5:14663600-14664400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
37	chr5:14663600-14664400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
38	chr5:14663600-14664400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr5:14663600-14664600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
40	chr5:14663600-14664600	Flanking Active TSS	Primary B cells from cord blood	blood
41	chr5:14663600-14664600	Flanking Active TSS	Primary hematopoietic stem cells	blood
42	chr5:14663600-14664600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr5:14663600-14664600	Flanking Active TSS	Hela-S3	cervix
44	chr5:14663600-14665200	Active TSS	ES-I3 Cell Line	embryonic stem cell
45	chr5:14663600-14665400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr5:14663600-14665600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr5:14663600-14666000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr5:14663600-14666000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr5:14663600-14666000	Active TSS	NHLF	lung
50	chr5:14663600-14666200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links