Variant report

Variant	rs10412787
Chromosome Location	chr19:19596117-19596118
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19573288..19575099-chr19:19594629..19597608,2	MCF-7	breast:
2	chr19:19590124..19591949-chr19:19596092..19599221,4	K562	blood:
3	chr19:19587218..19589971-chr19:19595669..19597695,2	K562	blood:
4	chr19:19587338..19590282-chr19:19595416..19599165,3	MCF-7	breast:
5	chr19:19585265..19586941-chr19:19595062..19597219,2	K562	blood:
6	chr19:19513509..19518475-chr19:19595979..19603373,11	K562	blood:
7	chr19:19515306..19517570-chr19:19594692..19597580,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167491	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10404656	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10407522	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10409927	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10419026	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10419240	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10426633	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13344439	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs16996085	0.96[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16996119	0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2304097	0.83[ASW][hapmap];0.85[LWK][hapmap];0.87[YRI][hapmap]
rs28434154	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28553975	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60455087	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs7254150	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73922883	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73922888	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs952609	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 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	chr19:19577800-19598000	Weak transcription	Ovary	ovary
2	chr19:19579200-19598000	Weak transcription	Small Intestine	intestine
3	chr19:19579400-19599400	Weak transcription	Brain Angular Gyrus	brain
4	chr19:19579800-19598600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr19:19579800-19599200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr19:19579800-19599800	Weak transcription	Brain Substantia Nigra	brain
7	chr19:19580600-19597200	Weak transcription	Brain Anterior Caudate	brain
8	chr19:19582200-19597600	Strong transcription	Dnd41	blood
9	chr19:19584200-19600000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr19:19587000-19599000	Weak transcription	Brain Germinal Matrix	brain
11	chr19:19587000-19599200	Weak transcription	Fetal Brain Female	brain
12	chr19:19587200-19599600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr19:19587600-19598600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr19:19588000-19598400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr19:19588800-19597200	Weak transcription	Pancreas	Pancrea
16	chr19:19588800-19597800	Weak transcription	Colonic Mucosa	Colon
17	chr19:19588800-19597800	Weak transcription	A549	lung
18	chr19:19588800-19599200	Weak transcription	Hela-S3	cervix
19	chr19:19589200-19597600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr19:19589200-19598000	Weak transcription	Esophagus	oesophagus
21	chr19:19589400-19598400	Weak transcription	Stomach Mucosa	stomach
22	chr19:19590400-19597400	Strong transcription	Duodenum Mucosa	Duodenum
23	chr19:19590400-19597800	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr19:19590400-19599400	Genic enhancers	Fetal Thymus	thymus
25	chr19:19590800-19598000	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr19:19591200-19598000	Genic enhancers	Fetal Muscle Leg	muscle
27	chr19:19591400-19598600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr19:19591400-19598800	Genic enhancers	Fetal Muscle Trunk	muscle
29	chr19:19591600-19596600	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr19:19592000-19599200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr19:19592200-19596200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr19:19592200-19596600	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr19:19592400-19600000	Weak transcription	Aorta	Aorta
34	chr19:19593200-19597200	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr19:19593200-19597400	Genic enhancers	Fetal Stomach	stomach
36	chr19:19593600-19598000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr19:19593600-19598600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr19:19593800-19598000	Weak transcription	Fetal Kidney	kidney
39	chr19:19594000-19598600	Weak transcription	Psoas Muscle	Psoas
40	chr19:19594200-19596400	Enhancers	NH-A	brain
41	chr19:19594200-19598400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr19:19594400-19598000	Weak transcription	Fetal Heart	heart
43	chr19:19594400-19598400	Weak transcription	Stomach Smooth Muscle	stomach
44	chr19:19594600-19596600	Weak transcription	HepG2	liver
45	chr19:19594600-19597400	Weak transcription	Gastric	stomach
46	chr19:19594800-19597800	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr19:19594800-19598200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr19:19594800-19599000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr19:19595000-19596200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr19:19595000-19596400	Weak transcription	Rectal Mucosa Donor 29	rectum

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