Variant report

Variant	rs28399619
Chromosome Location	chr19:45318644-45318645
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	POLR2A	chr19:45318612-45318647	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:45310566..45312166-chr19:45318337..45320547,2	K562	blood:
2	chr19:45309583..45313633-chr19:45318151..45320547,3	K562	blood:

Variant related genes	Relation type
BCAM	TF binding region
ENSG00000187244	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs28399624	0.84[AFR][1000 genomes]
rs5122	1.00[AMR][1000 genomes]
rs57838120	1.00[AMR][1000 genomes]
rs60170431	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912117	chr19:45298069-45322744	Weak transcription Bivalent Enhancer ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
2	nsv912118	chr19:45300056-45326664	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv912121	chr19:45304307-45319297	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv912122	chr19:45304307-45324516	Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv912125	chr19:45310319-45321841	Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv579863	chr19:45310319-45322451	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv912128	chr19:45312114-45321841	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:45313000-45319000	Weak transcription	Brain Cingulate Gyrus	brain
2	chr19:45313000-45320400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr19:45313000-45325400	Weak transcription	Brain Hippocampus Middle	brain
4	chr19:45313400-45321200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr19:45313400-45321600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr19:45313600-45322800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr19:45313600-45323400	Weak transcription	Colon Smooth Muscle	Colon
8	chr19:45313600-45326400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:45313600-45326600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr19:45314000-45321200	Weak transcription	Liver	Liver
11	chr19:45314000-45323400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr19:45314000-45323600	Weak transcription	HSMMtube	muscle
13	chr19:45314200-45319400	Genic enhancers	Fetal Muscle Trunk	muscle
14	chr19:45314200-45323200	Weak transcription	Right Atrium	heart
15	chr19:45314400-45319000	Strong transcription	NHEK	skin
16	chr19:45314600-45318800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr19:45314600-45319000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr19:45314600-45319200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr19:45314600-45322200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr19:45314600-45323800	Strong transcription	Fetal Stomach	stomach
21	chr19:45314600-45326200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr19:45314800-45319200	Strong transcription	Lung	lung
23	chr19:45314800-45319200	Strong transcription	Right Ventricle	heart
24	chr19:45315200-45319200	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr19:45315200-45320000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr19:45315400-45319000	Strong transcription	Gastric	stomach
27	chr19:45315800-45319000	Strong transcription	Skeletal Muscle Male	skeletal muscle
28	chr19:45315800-45321400	Weak transcription	Colonic Mucosa	Colon
29	chr19:45315800-45324200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr19:45316200-45319000	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr19:45316200-45319200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
32	chr19:45316400-45318800	Strong transcription	Left Ventricle	heart
33	chr19:45316400-45319200	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr19:45316400-45319200	Strong transcription	Adipose Nuclei	Adipose
35	chr19:45316600-45319200	Strong transcription	Fetal Intestine Large	intestine
36	chr19:45316600-45319200	Strong transcription	HMEC	breast
37	chr19:45316800-45318800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr19:45316800-45319000	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr19:45316800-45319000	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr19:45316800-45319000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr19:45316800-45319000	Strong transcription	Fetal Lung	lung
42	chr19:45316800-45319000	Strong transcription	Stomach Smooth Muscle	stomach
43	chr19:45316800-45321000	Strong transcription	Fetal Intestine Small	intestine
44	chr19:45316800-45324200	Genic enhancers	Fetal Muscle Leg	muscle
45	chr19:45317000-45318800	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr19:45317000-45321000	Weak transcription	Fetal Heart	heart
47	chr19:45317200-45319000	Strong transcription	Fetal Kidney	kidney
48	chr19:45317200-45323800	Weak transcription	Esophagus	oesophagus
49	chr19:45317400-45319200	Strong transcription	HepG2	liver
50	chr19:45317400-45323600	Weak transcription	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links