Variant report

Variant	rs17878918
Chromosome Location	chr19:39898196-39898197
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:34)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:34 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:64845658..64846400-chr19:39897421..39898419,2	Hela-S3	cervix:
2	chr12:110718990..110719930-chr19:39897745..39898520,2	Hela-S3	cervix:
3	chr19:39615191..39619693-chr19:39896201..39900336,5	K562	blood:
4	chr19:39845453..39848424-chr19:39895764..39898971,3	K562	blood:
5	chr19:39840535..39845164-chr19:39896257..39899085,6	K562	blood:
6	chr19:39657697..39659384-chr19:39897167..39900031,2	MCF-7	breast:
7	chr1:154154700..154155685-chr19:39897634..39898527,2	Hela-S3	cervix:
8	chr19:39897578..39898321-chr2:10587983..10588853,2	Hela-S3	cervix:
9	chr19:39870090..39872706-chr19:39896228..39899181,3	MCF-7	breast:
10	chr19:39897402..39898381-chr3:49977408..49978016,3	Hela-S3	cervix:
11	chr19:39897898..39898490-chr2:86332899..86333759,2	Hela-S3	cervix:
12	chr11:85955594..85956361-chr19:39897486..39898331,2	Hela-S3	cervix:
13	chr19:39897603..39899385-chr19:39988618..39990162,2	K562	blood:
14	chr17:26926062..26926808-chr19:39897565..39898385,2	Hela-S3	cervix:
15	chr19:39831462..39833819-chr19:39895852..39900331,6	MCF-7	breast:
16	chr19:39896779..39898859-chr5:65220597..65222904,2	K562	blood:
17	chr19:39897803..39898448-chr20:30192904..30193696,2	Hela-S3	cervix:
18	chr19:39898047..39898793-chr5:65439798..65440499,2	Hela-S3	cervix:
19	chr19:39897973..39898580-chr6:86387847..86388601,2	Hela-S3	cervix:
20	chr19:39694375..39697008-chr19:39898075..39900660,3	MCF-7	breast:
21	chr19:39897875..39898547-chrX:40944303..40945093,2	Hela-S3	cervix:
22	chr19:39846643..39848442-chr19:39897327..39899339,2	MCF-7	breast:
23	chr19:39897483..39899188-chr19:39966123..39968419,2	MCF-7	breast:
24	chr1:156252136..156252675-chr19:39897387..39898246,2	Hela-S3	cervix:
25	chr1:150336546..150337227-chr19:39897504..39898234,2	Hela-S3	cervix:
26	chr19:39897453..39898763-chr7:116502422..116503453,3	Hela-S3	cervix:
27	chr19:39830669..39836861-chr19:39895802..39900887,6	MCF-7	breast:
28	chr19:39844628..39846175-chr19:39896261..39898794,2	MCF-7	breast:
29	chr1:33815184..33816117-chr19:39897889..39898487,2	Hela-S3	cervix:
30	chr19:39897504..39898591-chr5:179050003..179050948,4	Hela-S3	cervix:
31	chr19:39874668..39877067-chr19:39896075..39898532,2	MCF-7	breast:
32	chr19:39897556..39898246-chr6:27861059..27861615,2	Hela-S3	cervix:
33	chr1:45272804..45273405-chr19:39897695..39898336,2	Hela-S3	cervix:
34	chr19:39828912..39834348-chr19:39896525..39904623,14	K562	blood:

No data

Variant related genes	Relation type
ENSG00000196235	Chromatin interaction
ENSG00000198952	Chromatin interaction
ENSG00000269961	Chromatin interaction
ENSG00000074266	Chromatin interaction
ENSG00000257135	Chromatin interaction
ENSG00000198898	Chromatin interaction
ENSG00000115758	Chromatin interaction
ENSG00000269246	Chromatin interaction
ENSG00000132300	Chromatin interaction
ENSG00000112851	Chromatin interaction
ENSG00000130755	Chromatin interaction
ENSG00000174437	Chromatin interaction
ENSG00000130669	Chromatin interaction
ENSG00000227543	Chromatin interaction
ENSG00000090932	Chromatin interaction
ENSG00000076382	Chromatin interaction
ENSG00000179751	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000068654	Chromatin interaction
ENSG00000143549	Chromatin interaction
ENSG00000153914	Chromatin interaction
ENSG00000188396	Chromatin interaction
ENSG00000233246	Chromatin interaction
ENSG00000004534	Chromatin interaction
ENSG00000169045	Chromatin interaction
ENSG00000203875	Chromatin interaction
ENSG00000179134	Chromatin interaction
ENSG00000125968	Chromatin interaction
ENSG00000134686	Chromatin interaction
ENSG00000183735	Chromatin interaction
ENSG00000163125	Chromatin interaction
ENSG00000124486	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs28535763	1.00[EUR][1000 genomes]
rs28605012	1.00[EUR][1000 genomes]
rs56222183	1.00[EUR][1000 genomes]
rs56904899	1.00[EUR][1000 genomes]
rs57536536	1.00[EUR][1000 genomes]
rs60577443	1.00[EUR][1000 genomes]
rs61112725	1.00[EUR][1000 genomes]
rs61179656	1.00[EUR][1000 genomes]
rs61213828	1.00[EUR][1000 genomes]
rs73546015	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911679	chr19:39735106-39924129	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
2	nsv1058514	chr19:39744112-39902580	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv911680	chr19:39792460-39924129	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	194 gene(s)	inside rSNPs	diseases
4	nsv870133	chr19:39822160-39938468	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
5	nsv911682	chr19:39847132-39914748	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
6	nsv911683	chr19:39847132-39924129	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	185 gene(s)	inside rSNPs	diseases
7	nsv911684	chr19:39886218-39923863	Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
8	nsv911685	chr19:39888449-39948779	Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	222 gene(s)	inside rSNPs	diseases
9	nsv911686	chr19:39891219-39907781	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	171 gene(s)	inside rSNPs	diseases
10	nsv911687	chr19:39891219-39909714	Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	171 gene(s)	inside rSNPs	diseases
11	nsv911688	chr19:39891219-39919538	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	172 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	chr19:39896200-39898600	Active TSS	Esophagus	oesophagus
2	chr19:39896400-39898400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr19:39896600-39898400	Active TSS	Right Ventricle	heart
4	chr19:39896600-39899200	Active TSS	NHDF-Ad	bronchial
5	chr19:39896600-39901400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr19:39896600-39901600	Active TSS	Psoas Muscle	Psoas
7	chr19:39896800-39898200	Active TSS	Sigmoid Colon	Sigmoid Colon
8	chr19:39896800-39898400	Bivalent/Poised TSS	Fetal Brain Female	brain
9	chr19:39896800-39898400	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr19:39896800-39898400	Active TSS	Left Ventricle	heart
11	chr19:39896800-39898400	Active TSS	Lung	lung
12	chr19:39896800-39898400	Active TSS	Small Intestine	intestine
13	chr19:39896800-39898600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr19:39896800-39898600	Active TSS	Brain Cingulate Gyrus	brain
15	chr19:39896800-39898600	Active TSS	Brain Hippocampus Middle	brain
16	chr19:39896800-39899000	Active TSS	H9 Cell Line	embryonic stem cell
17	chr19:39896800-39899400	Active TSS	Brain Angular Gyrus	brain
18	chr19:39896800-39899400	Active TSS	Brain Inferior Temporal Lobe	brain
19	chr19:39896800-39900000	Active TSS	Right Atrium	heart
20	chr19:39897000-39898200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr19:39897000-39898200	Active TSS	Rectal Mucosa Donor 29	rectum
22	chr19:39897000-39898200	Active TSS	Thymus	Thymus
23	chr19:39897000-39898400	Active TSS	H1 Cell Line	embryonic stem cell
24	chr19:39897000-39898400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr19:39897000-39898400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
26	chr19:39897000-39898400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
27	chr19:39897000-39898400	Active TSS	Duodenum Mucosa	Duodenum
28	chr19:39897000-39898400	Active TSS	Fetal Heart	heart
29	chr19:39897000-39898400	Active TSS	Gastric	stomach
30	chr19:39897000-39898400	Active TSS	Skeletal Muscle Female	skeletal muscle
31	chr19:39897000-39898400	Active TSS	Spleen	Spleen
32	chr19:39897000-39898600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr19:39897000-39898600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr19:39897000-39898600	Active TSS	Primary T cells from cord blood	blood
35	chr19:39897000-39898600	Active TSS	GM12878-XiMat	blood
36	chr19:39897000-39899000	Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr19:39897000-39899800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
38	chr19:39897000-39900600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr19:39897000-39900800	Active TSS	Liver	Liver
40	chr19:39897000-39901000	Active TSS	Fetal Kidney	kidney
41	chr19:39897000-39901000	Active TSS	Ovary	ovary
42	chr19:39897000-39901200	Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr19:39897200-39898200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr19:39897200-39898200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr19:39897200-39898200	Active TSS	Primary T cells fromperipheralblood	blood
46	chr19:39897200-39898200	Active TSS	Primary hematopoietic stem cells short term culture	blood
47	chr19:39897200-39898200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr19:39897200-39898400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr19:39897200-39898400	Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr19:39897200-39898400	Active TSS	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links