Variant report

Variant	rs55982633
Chromosome Location	chr15:50717205-50717206
allele	C/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	CHD1	chr15:50716738-50717244	H1-hESC	embryonic stem cell:	n/a	n/a
2	PML	chr15:50715965-50717225	GM12878	blood:	n/a	chr15:50716396-50716404
3	MAX	chr15:50716024-50717248	MCF-7	breast:	n/a	n/a
4	POLR2A	chr15:50715425-50717621	GM12891	blood:	n/a	n/a
5	NR2F2	chr15:50715923-50717234	K562	blood:	n/a	n/a
6	ELF1	chr15:50715494-50717916	MCF-7	breast:	n/a	chr15:50716333-50716344 chr15:50716333-50716344 chr15:50717174-50717185 chr15:50717015-50717026 chr15:50716334-50716343 chr15:50716533-50716545 chr15:50717016-50717025 chr15:50717015-50717026
7	POLR2A	chr15:50715954-50717759	IMR90	lung:	n/a	n/a
8	MXI1	chr15:50715874-50717257	SK-N-SH	brain:	n/a	n/a
9	MYBL2	chr15:50715550-50717214	HepG2	liver:	n/a	n/a
10	POLR2A	chr15:50715464-50717416	MCF10A-Er-Src	breast:	n/a	n/a
11	MXI1	chr15:50716202-50717329	GM12878	blood:	n/a	n/a
12	REST	chr15:50715920-50717266	H1-neurons	neurons:	n/a	chr15:50716814-50716834 chr15:50716348-50716361 chr15:50716462-50716475
13	SIN3A	chr15:50716142-50717621	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr15:50715245-50717511	HepG2	liver:	n/a	n/a
15	GABPA	chr15:50716087-50717224	A549	lung:	n/a	n/a
16	BRCA1	chr15:50717172-50717407	Hela-S3	cervix:	n/a	n/a
17	GABPA	chr15:50715789-50717432	MCF-7	breast:	n/a	n/a
18	SPI1	chr15:50716948-50717408	HL-60	blood:	n/a	chr15:50717015-50717028
19	ELK1	chr15:50716246-50717241	K562	blood:	n/a	chr15:50717015-50717024 chr15:50717015-50717024
20	EBF1	chr15:50716182-50717369	GM12878	blood:	n/a	n/a
21	WRNIP1	chr15:50716194-50717785	GM12878	blood:	n/a	n/a
22	HCFC1	chr15:50716003-50717764	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr15:50717158-50717729	HepG2	liver:	n/a	n/a
24	SIN3AK20	chr15:50715727-50717907	MCF-7	breast:	n/a	n/a
25	ELK1	chr15:50716237-50717407	GM12878	blood:	n/a	chr15:50717015-50717024 chr15:50717015-50717024
26	ELK4	chr15:50716114-50717491	Hela-S3	cervix:	n/a	chr15:50717016-50717024 chr15:50717015-50717024
27	SIN3AK20	chr15:50716069-50717276	MCF-7	breast:	n/a	n/a
28	POLR2A	chr15:50715482-50717811	MCF10A-Er-Src	breast:	n/a	n/a
29	ZNF384	chr15:50716206-50717366	K562	blood:	n/a	n/a
30	MXI1	chr15:50716130-50717653	IMR90	lung:	n/a	n/a
31	ZNF384	chr15:50716517-50717300	GM12878	blood:	n/a	n/a
32	SRF	chr15:50716006-50717247	MCF-7	breast:	n/a	n/a
33	UBTF	chr15:50716146-50717393	K562	blood:	n/a	n/a
34	POLR2A	chr15:50715512-50717738	HepG2	liver:	n/a	n/a
35	ELF1	chr15:50715917-50717242	HCT-116	colon:	n/a	chr15:50716333-50716344 chr15:50716333-50716344 chr15:50717174-50717185 chr15:50717015-50717026 chr15:50716334-50716343 chr15:50716533-50716545 chr15:50717016-50717025 chr15:50717015-50717026

No.	Distal block	Cell Line	Cell type
1	chr1:161359042..161360035-chr15:50716770..50717404,2	Hela-S3	cervix:
2	chr15:50644978..50654282-chr15:50714279..50723145,48	MCF-7	breast:
3	chr15:50644601..50650486-chr15:50714318..50720349,10	K562	blood:
4	chr15:50714855..50718759-chr15:50728296..50731650,9	MCF-7	breast:
5	chr15:50644770..50653815-chr15:50713287..50720249,51	MCF-7	breast:
6	chr15:50644809..50652796-chr15:50713240..50720627,20	K562	blood:
7	chr15:50647576..50648414-chr15:50716378..50717277,2	MCF-7	breast:
8	chr15:50715057..50718112-chr15:51199966..51202837,4	MCF-7	breast:
9	chr15:50716729..50717278-chr17:76837130..76837665,2	Hela-S3	cervix:
10	chr15:50716224..50718029-chr15:52121423..52123385,2	MCF-7	breast:

Variant related genes	Relation type
USP8	TF binding region
ENSG00000081014	Chromatin interaction
ENSG00000138592	Chromatin interaction
ENSG00000244879	Chromatin interaction
ENSG00000138594	Chromatin interaction
ENSG00000055483	Chromatin interaction
ENSG00000104064	Chromatin interaction
ENSG00000264109	Chromatin interaction
ENSG00000259715	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs2241769	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28376390	0.82[AFR][1000 genomes]
rs3098204	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3131565	0.91[EUR][1000 genomes]
rs3131571	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3131572	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3131575	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3131612	0.81[EUR][1000 genomes]
rs3131613	0.80[EUR][1000 genomes]
rs4318151	0.83[ASN][1000 genomes]
rs62016946	0.91[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	nsv1045456	chr15:50592472-51019873	Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
2	nsv948579	chr15:50645530-51045564	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
3	nsv524613	chr15:50656449-50868779	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv904210	chr15:50702058-50786024	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv1040717	chr15:50715572-50846521	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv1053966	chr15:50715572-51133186	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
7	nsv542383	chr15:50715572-51133186	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
8	nsv1043805	chr15:50715572-51208891	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
9	nsv542384	chr15:50715572-51208891	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 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	chr15:50715600-50717400	Active TSS	NH-A	brain
2	chr15:50715600-50717400	Active TSS	NHEK	skin
3	chr15:50715600-50717600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr15:50715600-50718000	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr15:50715600-50718400	Active TSS	Hela-S3	cervix
6	chr15:50715800-50717400	Active TSS	Primary T helper naive cells from peripheral blood	blood
7	chr15:50715800-50717400	Active TSS	Brain Anterior Caudate	brain
8	chr15:50715800-50717400	Active TSS	Brain Cingulate Gyrus	brain
9	chr15:50715800-50717400	Active TSS	Colon Smooth Muscle	Colon
10	chr15:50715800-50717400	Active TSS	Fetal Brain Female	brain
11	chr15:50715800-50717400	Active TSS	Thymus	Thymus
12	chr15:50715800-50717600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:50715800-50717600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr15:50715800-50717600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr15:50715800-50717800	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr15:50715800-50717800	Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr15:50715800-50717800	Active TSS	HSMM	muscle
18	chr15:50715800-50717800	Active TSS	HSMMtube	muscle
19	chr15:50715800-50718000	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr15:50715800-50718000	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr15:50715800-50718200	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr15:50715800-50718200	Active TSS	Colonic Mucosa	Colon
23	chr15:50715800-50718200	Active TSS	Right Atrium	heart
24	chr15:50715800-50718400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr15:50715800-50718400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr15:50715800-50718400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr15:50716000-50717400	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr15:50716000-50717400	Active TSS	iPS-18 Cell Line	embryonic stem cell
29	chr15:50716000-50717400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr15:50716000-50717400	Active TSS	Aorta	Aorta
31	chr15:50716000-50717400	Active TSS	Fetal Kidney	kidney
32	chr15:50716000-50717400	Active TSS	Pancreas	Pancrea
33	chr15:50716000-50717400	Active TSS	Osteobl	bone
34	chr15:50716000-50717600	Active TSS	H1 Cell Line	embryonic stem cell
35	chr15:50716000-50717600	Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr15:50716000-50717600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr15:50716000-50717600	Active TSS	Primary T killer memory cells from peripheral blood	blood
38	chr15:50716000-50717600	Active TSS	Muscle Satellite Cultured Cells	--
39	chr15:50716000-50717600	Active TSS	Fetal Muscle Leg	muscle
40	chr15:50716000-50717600	Active TSS	Ovary	ovary
41	chr15:50716000-50717600	Active TSS	Sigmoid Colon	Sigmoid Colon
42	chr15:50716000-50717600	Active TSS	NHLF	lung
43	chr15:50716000-50717800	Active TSS	H9 Cell Line	embryonic stem cell
44	chr15:50716000-50717800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr15:50716000-50717800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr15:50716000-50717800	Active TSS	Fetal Intestine Small	intestine
47	chr15:50716000-50717800	Active TSS	Left Ventricle	heart
48	chr15:50716000-50717800	Active TSS	Psoas Muscle	Psoas
49	chr15:50716000-50717800	Active TSS	Right Ventricle	heart
50	chr15:50716000-50718000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links