Variant report

Variant	rs7248421
Chromosome Location	chr19:45606125-45606126
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:45580658..45583147-chr19:45605476..45608233,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000007047	Chromatin interaction
ENSG00000142252	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10401157	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10401823	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10405086	0.97[EUR][1000 genomes]
rs10416500	0.90[ASN][1000 genomes]
rs10420562	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10425074	0.97[ASN][1000 genomes]
rs1048699	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1114831	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1114832	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12459074	0.92[ASN][1000 genomes]
rs12462040	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17643262	0.87[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs2004357	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2041262	0.90[ASN][1000 genomes]
rs28469095	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28620490	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34545713	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3925162	0.97[ASN][1000 genomes]
rs57565080	0.87[ASN][1000 genomes]
rs754366	0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3449420	chr19:45523560-45626884	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv912142	chr19:45570051-45708758	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv833842	chr19:45593888-45684308	Bivalent Enhancer Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv833843	chr19:45593888-45793682	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:45597400-45609400	Enhancers	Stomach Mucosa	stomach
2	chr19:45597600-45606200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:45597600-45609200	Enhancers	Pancreas	Pancrea
4	chr19:45598400-45606600	Genic enhancers	Fetal Intestine Small	intestine
5	chr19:45600000-45606200	Enhancers	Fetal Intestine Large	intestine
6	chr19:45600000-45607800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr19:45600800-45607800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:45601400-45606200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr19:45601400-45608000	Enhancers	Esophagus	oesophagus
10	chr19:45601400-45608000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr19:45601600-45606400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr19:45602000-45606200	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr19:45602000-45606200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr19:45602000-45612200	Weak transcription	Hela-S3	cervix
15	chr19:45602200-45606400	Weak transcription	Colon Smooth Muscle	Colon
16	chr19:45602400-45607200	Enhancers	NHLF	lung
17	chr19:45602400-45607600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr19:45602600-45606200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr19:45602600-45606200	Weak transcription	Fetal Lung	lung
20	chr19:45602600-45606200	Weak transcription	Ovary	ovary
21	chr19:45602600-45606400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr19:45602800-45606200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr19:45602800-45612600	Weak transcription	A549	lung
24	chr19:45603400-45606200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr19:45603400-45609200	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr19:45603600-45606400	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr19:45603600-45606400	Enhancers	Fetal Thymus	thymus
28	chr19:45603600-45607600	Enhancers	Duodenum Mucosa	Duodenum
29	chr19:45603600-45609200	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr19:45603600-45612600	Weak transcription	Dnd41	blood
31	chr19:45603800-45606200	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr19:45603800-45606200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr19:45603800-45606200	Enhancers	Primary T cells fromperipheralblood	blood
34	chr19:45603800-45606400	Enhancers	Rectal Mucosa Donor 29	rectum
35	chr19:45603800-45608400	Enhancers	Small Intestine	intestine
36	chr19:45603800-45619600	Weak transcription	HSMMtube	muscle
37	chr19:45604000-45606400	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr19:45604000-45606400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr19:45604000-45608000	Enhancers	Fetal Muscle Trunk	muscle
40	chr19:45604000-45609600	Enhancers	Fetal Muscle Leg	muscle
41	chr19:45604200-45607400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr19:45604200-45609200	Enhancers	Spleen	Spleen
43	chr19:45604200-45611200	Weak transcription	K562	blood
44	chr19:45604400-45606200	Weak transcription	Brain Substantia Nigra	brain
45	chr19:45604400-45606200	Weak transcription	NHEK	skin
46	chr19:45604400-45606400	Weak transcription	HSMM	muscle
47	chr19:45604400-45606600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr19:45604400-45608000	Enhancers	Fetal Kidney	kidney
49	chr19:45604600-45606200	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr19:45604600-45606200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links