Variant report

Variant	rs888997
Chromosome Location	chr19:39144714-39144715
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39143284..39145449-chr19:39147356..39150112,2	K562	blood:
2	chr19:39141727..39145361-chr19:39153035..39156463,3	K562	blood:
3	chr19:39144043..39146811-chr19:39176683..39178531,2	MCF-7	breast:
4	chr19:39136970..39140096-chr19:39140173..39145438,10	MCF-7	breast:
5	chr19:39137026..39140722-chr19:39142479..39146305,6	K562	blood:

Variant related genes	Relation type
ENSG00000130402	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1031849	0.83[EUR][1000 genomes]
rs10424568	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1060186	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs11665964	0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11670636	0.80[ASN][1000 genomes]
rs12462503	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12984247	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1564203	0.88[CEU][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes]
rs1985636	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2080988	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2112649	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2112651	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3786841	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3786843	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4347742	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4801861	0.82[CEU][hapmap];0.87[JPT][hapmap]
rs4802743	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6508813	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6508814	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7252630	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs749701	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs752067	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs755690	0.86[ASN][1000 genomes]
rs8099948	0.87[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8107877	0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs888996	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9304576	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9304577	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs936524	0.88[CEU][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs888997	CAPN12	cis	Muscle Skeletal	GTEx
rs888997	CTD-2540F13.2	cis	Adipose Subcutaneous	GTEx
rs888997	CAPN12	cis	Heart Left Ventricle	GTEx
rs888997	CAPN12	cis	Adipose Subcutaneous	GTEx
rs888997	CAPN12	cis	Esophagus Muscularis	GTEx
rs888997	CTD-2540F13.2	cis	Nerve Tibial	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	chr19:39140400-39146800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr19:39140600-39151000	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr19:39140800-39145200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr19:39141200-39145600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr19:39141200-39147000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
7	chr19:39141200-39147600	Enhancers	Primary hematopoietic stem cells	blood
8	chr19:39141200-39148600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr19:39141200-39148800	Enhancers	Placenta Amnion	Placenta Amnion
10	chr19:39141200-39162800	Enhancers	Psoas Muscle	Psoas
11	chr19:39141400-39145400	Enhancers	Fetal Kidney	kidney
12	chr19:39141400-39146000	Enhancers	Brain Anterior Caudate	brain
13	chr19:39141400-39146400	Enhancers	H1 Cell Line	embryonic stem cell
14	chr19:39141400-39147000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr19:39141400-39147800	Enhancers	Small Intestine	intestine
16	chr19:39141400-39148000	Genic enhancers	Fetal Muscle Leg	muscle
17	chr19:39141600-39145200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr19:39141800-39146800	Enhancers	Fetal Lung	lung
19	chr19:39141800-39147200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr19:39142000-39144800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr19:39142000-39147000	Enhancers	Brain Angular Gyrus	brain
22	chr19:39142000-39149400	Enhancers	Liver	Liver
23	chr19:39142200-39145400	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr19:39142200-39145600	Weak transcription	Fetal Brain Female	brain
25	chr19:39142200-39146800	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr19:39142200-39151800	Enhancers	Brain Cingulate Gyrus	brain
27	chr19:39142400-39149400	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr19:39142600-39150400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr19:39142800-39145000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
30	chr19:39142800-39151200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr19:39143000-39146400	Enhancers	Fetal Brain Male	brain
32	chr19:39143000-39149800	Enhancers	H9 Cell Line	embryonic stem cell
33	chr19:39143200-39146800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr19:39143400-39144800	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr19:39143400-39144800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr19:39143400-39144800	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr19:39143400-39144800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr19:39143400-39144800	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr19:39143400-39145200	Enhancers	Fetal Heart	heart
40	chr19:39143400-39145200	Weak transcription	Dnd41	blood
41	chr19:39143400-39145200	Weak transcription	GM12878-XiMat	blood
42	chr19:39143400-39145200	Enhancers	NH-A	brain
43	chr19:39143400-39145400	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr19:39143400-39145600	Weak transcription	Gastric	stomach
45	chr19:39143400-39146800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr19:39143400-39148400	Enhancers	Brain Substantia Nigra	brain
47	chr19:39143400-39149200	Enhancers	Brain Hippocampus Middle	brain
48	chr19:39143400-39150600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr19:39143400-39154400	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr19:39143600-39144800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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