Variant report

Variant	rs888996
Chromosome Location	chr19:39150622-39150623
allele	A/C
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39150052..39153067-chr19:39197622..39201361,3	MCF-7	breast:
2	chr19:39148794..39150832-chr3:147109413..147111570,2	MCF-7	breast:
3	chr19:39148867..39151861-chr19:39164065..39166508,2	K562	blood:
4	chr19:39145586..39147740-chr19:39150423..39154465,3	K562	blood:
5	chr19:39150082..39153309-chr19:39178166..39180062,3	MCF-7	breast:
6	chr19:39149024..39154711-chr19:39158901..39163144,7	MCF-7	breast:
7	chr19:39147918..39151863-chr19:39340642..39342980,4	MCF-7	breast:
8	chr19:39147345..39151436-chr19:39186794..39189528,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000130402	Chromatin interaction
ENSG00000174963	Chromatin interaction
ENSG00000152977	Chromatin interaction
ENSG00000104824	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1031849	0.80[ASN][1000 genomes]
rs10424568	0.96[ASN][1000 genomes]
rs11665964	0.81[ASN][1000 genomes]
rs12462503	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12984247	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1564203	0.81[ASN][1000 genomes]
rs1985636	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2080988	0.82[ASN][1000 genomes]
rs2112649	0.82[ASN][1000 genomes]
rs2112651	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3786841	0.81[ASN][1000 genomes]
rs3786843	0.80[ASN][1000 genomes]
rs4347742	0.82[ASN][1000 genomes]
rs4802743	0.82[ASN][1000 genomes]
rs6508813	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6508814	0.83[ASN][1000 genomes]
rs7252630	0.82[ASN][1000 genomes]
rs749701	0.80[ASN][1000 genomes]
rs752067	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs755690	0.83[ASN][1000 genomes]
rs8099948	0.81[ASN][1000 genomes]
rs888997	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9304576	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833826	chr19:38945106-39184547	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv833827	chr19:38993054-39184547	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv833828	chr19:39084759-39257979	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
5	nsv1057901	chr19:39112486-39174332	Genic enhancers Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs888996	CTD-2540F13.2	cis	Nerve Tibial	GTEx
rs888996	CAPN12	cis	Adipose Subcutaneous	GTEx
rs888996	CAPN12	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39138600-39152200	Transcr. at gene 5' and 3'	A549	lung
2	chr19:39140600-39151000	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr19:39141200-39162800	Enhancers	Psoas Muscle	Psoas
4	chr19:39142200-39151800	Enhancers	Brain Cingulate Gyrus	brain
5	chr19:39142800-39151200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr19:39143400-39154400	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr19:39143800-39153200	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr19:39144200-39153400	Genic enhancers	K562	blood
9	chr19:39144400-39152200	Enhancers	Right Ventricle	heart
10	chr19:39144600-39154000	Enhancers	Right Atrium	heart
11	chr19:39144800-39154000	Genic enhancers	Fetal Intestine Large	intestine
12	chr19:39145200-39153400	Genic enhancers	Fetal Intestine Small	intestine
13	chr19:39146800-39151800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr19:39147000-39151400	Enhancers	Brain Anterior Caudate	brain
15	chr19:39147400-39151400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr19:39147400-39160000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr19:39147600-39151400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr19:39147600-39151600	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr19:39147600-39154000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr19:39147600-39154000	Enhancers	Brain Angular Gyrus	brain
21	chr19:39147800-39151000	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr19:39147800-39151200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr19:39147800-39160800	Enhancers	Placenta	Placenta
24	chr19:39148000-39151000	Enhancers	Fetal Kidney	kidney
25	chr19:39148000-39152800	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr19:39148200-39151400	Enhancers	Small Intestine	intestine
27	chr19:39148600-39151800	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr19:39148600-39153400	Genic enhancers	HUES6 Cell Line	embryonic stem cell
29	chr19:39148800-39151200	Enhancers	Fetal Stomach	stomach
30	chr19:39148800-39151200	Weak transcription	Lung	lung
31	chr19:39148800-39151400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr19:39148800-39153000	Weak transcription	Primary B cells from cord blood	blood
33	chr19:39149000-39150800	Weak transcription	Primary B cells from peripheral blood	blood
34	chr19:39149000-39151400	Enhancers	Primary T cells fromperipheralblood	blood
35	chr19:39149000-39151400	Enhancers	Duodenum Mucosa	Duodenum
36	chr19:39149000-39154200	Enhancers	Brain Substantia Nigra	brain
37	chr19:39149000-39154600	Weak transcription	Primary T cells from cord blood	blood
38	chr19:39149000-39155200	Weak transcription	Fetal Brain Female	brain
39	chr19:39149200-39152000	Enhancers	Stomach Mucosa	stomach
40	chr19:39149200-39153400	Genic enhancers	Fetal Muscle Leg	muscle
41	chr19:39149400-39151400	Weak transcription	Dnd41	blood
42	chr19:39149400-39152600	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr19:39149600-39151200	Enhancers	HepG2	liver
44	chr19:39149600-39151400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr19:39149600-39151400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr19:39149600-39151400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr19:39149600-39151400	Enhancers	Adipose Nuclei	Adipose
48	chr19:39149600-39151400	Enhancers	Esophagus	oesophagus
49	chr19:39149600-39151600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr19:39149600-39152200	Enhancers	Ovary	ovary

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