Variant report

Variant	rs55678338
Chromosome Location	chr19:55893203-55893204
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:55893203-55893253	HNPCEpiC	eye:	n/a
2	chr19:55893203-55893253	LNCaP	prostate:	n/a
3	chr19:55893203-55893253	GM12891	blood:	n/a
4	chr19:55893203-55893253	PFSK-1	brain:	n/a
5	chr19:55893203-55893253	HAEpiC	amniotic membrane:	n/a
6	chr19:55893203-55893253	Jurkat	blood:	n/a
7	chr19:55893203-55893253	HPAEpiC	pulmonary alveolar:	n/a
8	chr19:55893203-55893253	HRPEpiC	eye:	n/a
9	chr19:55893203-55893253	HEEpiC	esophagus:	n/a
10	chr19:55893203-55893253	BE2_C	brain:	n/a
11	chr19:55893203-55893253	ECC-1	luminal epithelium:	n/a
12	chr19:55893203-55893253	NH-A	brain:	n/a
13	chr19:55893203-55893253	HepG2	liver:	n/a
14	chr19:55893203-55893253	AG09309	skin:	n/a
15	chr19:55893203-55893253	HCF	heart:	n/a
16	chr19:55893203-55893253	NT2-D1	testis:	n/a
17	chr19:55893203-55893253	HMEC	breast:	n/a
18	chr19:55893203-55893253	IMR90	lung:	fetal
19	chr19:55893203-55893253	NB4	blood:	n/a
20	chr19:55893203-55893253	Hepatocyte	liver:	n/a
21	chr19:55893203-55893253	AG04450	lung:	fetal
22	chr19:55893203-55893253	U87	brain:	n/a
23	chr19:55893203-55893253	HL-60	blood:	n/a
24	chr19:55893203-55893253	PANC-1	pancreas:	n/a
25	chr19:55893203-55893253	NHBE	bronchial:	n/a
26	chr19:55893203-55893253	HIPEpiC	eye:	n/a
27	chr19:55893203-55893253	HCM	heart:	n/a
28	chr19:55893203-55893253	MCF-7	breast:	n/a
29	chr19:55893203-55893253	AG10803	skin:	n/a
30	chr19:55893203-55893253	HUVEC	blood vessel:	n/a
31	chr19:55893203-55893253	SK-N-MC	brain:	n/a
32	chr19:55893203-55893253	SK-N-SH	brain:	n/a
33	chr19:55893203-55893253	CMK	blood:	n/a
34	chr19:55893203-55893253	NHDF-neo	bronchial:	n/a
35	chr19:55893203-55893253	GM12878	blood:	n/a
36	chr19:55893203-55893253	GM19239	blood:	n/a
37	chr19:55893203-55893253	H1-hESC	embryonic stem cell:	embryo
38	chr19:55893203-55893253	BJ	skin:	n/a
39	chr19:55893203-55893253	ProgFib	skin:	n/a
40	chr19:55893203-55893253	PrEC	prostate:	n/a
41	chr19:55893203-55893253	MCF10A-Er-Src	breast:	n/a
42	chr19:55893203-55893253	SKMC	muscle:	n/a
43	chr19:55893203-55893253	HCPEpiC	choroid plexus:	n/a
44	chr19:55893203-55893253	HRE	kidney:	n/a
45	chr19:55893203-55893253	GM12892	blood:	n/a
46	chr19:55893203-55893253	RPTEC	kidney:	n/a
47	chr19:55893203-55893253	Caco-2	colon:	n/a
48	chr19:55893203-55893253	T-47D	breast:	n/a
49	chr19:55893203-55893253	GM06990	blood:	n/a
50	chr19:55893203-55893253	K562	blood:	n/a

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:55892436..55894364-chr19:55964923..55967093,2	MCF-7	breast:
2	chr19:55764902..55773441-chr19:55891413..55900303,21	K562	blood:
3	chr19:55774813..55777090-chr19:55892887..55895596,2	MCF-7	breast:
4	chr19:55854922..55862011-chr19:55892906..55898744,13	MCF-7	breast:
5	chr19:55763551..55774813-chr19:55891413..55900376,23	K562	blood:
6	chr19:55848915..55854876-chr19:55892600..55899757,13	MCF-7	breast:

No data

Variant related genes	Relation type
RPL28	CpG island
ENSG00000269275	CpG island
ENSG00000063241	Chromatin interaction
ENSG00000105063	Chromatin interaction
ENSG00000267531	Chromatin interaction
ENSG00000133247	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs36047409	1.00[ASN][1000 genomes]
rs45477992	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55776192	1.00[ASN][1000 genomes]
rs57114796	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60231521	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73932623	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1816335	chr19:55683977-55901099	Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv1065760	chr19:55721521-55929740	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
3	nsv912456	chr19:55725410-55925500	Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
4	nsv912457	chr19:55725410-56019597	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	228 gene(s)	inside rSNPs	diseases
5	nsv432086	chr19:55807586-56050844	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	220 gene(s)	inside rSNPs	diseases
6	nsv912460	chr19:55814881-55897327	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
7	nsv912461	chr19:55845386-55897327	Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
8	nsv470162	chr19:55845386-55902257	Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
9	nsv912462	chr19:55845386-55925500	Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
10	nsv912463	chr19:55845386-56004901	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
11	nsv912464	chr19:55850269-55921164	Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
12	nsv516199	chr19:55854313-55901099	Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
13	nsv912465	chr19:55854313-55935184	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
14	nsv912470	chr19:55872591-55897170	Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	79 gene(s)	inside rSNPs	diseases
15	nsv912473	chr19:55874642-56145428	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
16	nsv544085	chr19:55875808-55911275	Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
17	nsv912476	chr19:55876747-55897327	Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	91 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55881400-55894800	Weak transcription	Right Atrium	heart
2	chr19:55887000-55893600	Weak transcription	GM12878-XiMat	blood
3	chr19:55888000-55894000	Weak transcription	Esophagus	oesophagus
4	chr19:55888000-55894200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr19:55888000-55894200	Weak transcription	NHEK	skin
6	chr19:55888200-55893800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr19:55888600-55893800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr19:55888800-55894600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr19:55889200-55894200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr19:55889200-55894200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr19:55889400-55894000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr19:55889400-55894000	Weak transcription	Colonic Mucosa	Colon
13	chr19:55889400-55894200	Weak transcription	Thymus	Thymus
14	chr19:55889600-55893400	Weak transcription	Gastric	stomach
15	chr19:55889600-55893600	Weak transcription	Duodenum Mucosa	Duodenum
16	chr19:55889600-55894200	Weak transcription	Primary T cells from cord blood	blood
17	chr19:55889600-55894400	Weak transcription	Lung	lung
18	chr19:55889600-55894600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr19:55889600-55894600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr19:55889600-55894800	Weak transcription	Ovary	ovary
21	chr19:55889600-55894800	Weak transcription	Right Ventricle	heart
22	chr19:55889600-55894800	Weak transcription	NH-A	brain
23	chr19:55890200-55894200	Weak transcription	Fetal Thymus	thymus
24	chr19:55890600-55894600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr19:55891000-55893600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr19:55891000-55894800	Weak transcription	HSMMtube	muscle
27	chr19:55891400-55893600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr19:55891400-55894800	Weak transcription	Brain Angular Gyrus	brain
29	chr19:55891600-55893600	Weak transcription	A549	lung
30	chr19:55891600-55894200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr19:55891600-55894200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr19:55892000-55894800	Weak transcription	HSMM	muscle
33	chr19:55892400-55893800	Weak transcription	Fetal Intestine Small	intestine
34	chr19:55893000-55893600	Enhancers	Dnd41	blood
35	chr19:55893000-55893600	Enhancers	Hela-S3	cervix
36	chr19:55893000-55894200	Enhancers	K562	blood
37	chr19:55893000-55894800	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr19:55893200-55893400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr19:55893200-55894400	Enhancers	Pancreas	Pancrea

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