Variant report

Variant	rs12610715
Chromosome Location	chr19:18872917-18872918
allele	A/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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:18872893..18875697-chr19:18882255..18885154,3	K562	blood:
2	chr19:18871848..18875156-chr19:18958149..18962324,3	MCF-7	breast:
3	chr19:18872280..18874058-chr19:18875721..18877942,2	K562	blood:
4	chr19:18817809..18819429-chr19:18870593..18873534,2	K562	blood:
5	chr19:18871674..18877764-chr19:18941611..18944793,8	MCF-7	breast:
6	chr19:18698038..18701680-chr19:18871708..18876325,4	MCF-7	breast:
7	chr19:18850574..18852890-chr19:18872787..18874422,2	MCF-7	breast:
8	chr19:18871687..18873296-chr19:18902854..18904707,2	K562	blood:
9	chr19:18870939..18874393-chr19:18880891..18884854,3	K562	blood:
10	chr19:18841548..18843285-chr19:18871994..18874440,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000005007	Chromatin interaction
ENSG00000006015	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10423674	0.81[GIH][hapmap]
rs11668545	0.81[EUR][1000 genomes]
rs11878358	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11880800	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs12460629	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs12462498	0.85[GIH][hapmap];0.80[MEX][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs2023878	0.85[GIH][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs2240012	0.90[CEU][hapmap];0.82[JPT][hapmap];0.94[EUR][1000 genomes]
rs2240013	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[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	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription 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 miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv911282	chr19:18624964-18928480	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv911293	chr19:18872917-19050957	Flanking Active TSS Genic enhancers Strong transcription Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv911294	chr19:18872917-19093619	Active TSS Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12610715	TMEM59L	cis	cerebellum	SCAN
rs12610715	CRTC1	cis	cerebellum	SCAN
rs12610715	ANKLE1	cis	parietal	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18849200-18873000	Weak transcription	Psoas Muscle	Psoas
2	chr19:18854400-18873200	Weak transcription	NHLF	lung
3	chr19:18854600-18895800	Weak transcription	Right Atrium	heart
4	chr19:18857200-18873600	Weak transcription	Fetal Kidney	kidney
5	chr19:18861200-18873000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:18861600-18873000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr19:18861600-18873000	Weak transcription	Brain Angular Gyrus	brain
8	chr19:18861600-18875200	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr19:18862000-18875200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr19:18862600-18888400	Weak transcription	Aorta	Aorta
11	chr19:18862800-18873000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr19:18864600-18873200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr19:18864600-18873200	Weak transcription	Osteobl	bone
14	chr19:18864600-18887400	Weak transcription	Primary B cells from cord blood	blood
15	chr19:18864800-18873000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr19:18864800-18875200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr19:18865000-18885000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr19:18865200-18873000	Weak transcription	Left Ventricle	heart
19	chr19:18865400-18875200	Weak transcription	Primary B cells from peripheral blood	blood
20	chr19:18865400-18879600	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr19:18865400-18880000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr19:18865400-18887400	Weak transcription	Primary T cells from cord blood	blood
23	chr19:18865600-18873200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr19:18865600-18878600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr19:18865600-18894600	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr19:18865600-18896000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr19:18865800-18873000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr19:18868000-18873000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr19:18868000-18873000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr19:18868000-18873600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr19:18868000-18877400	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr19:18868000-18878400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr19:18868000-18885400	Weak transcription	Thymus	Thymus
34	chr19:18868200-18875600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr19:18868200-18890600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr19:18868600-18873600	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr19:18868600-18878600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr19:18869800-18873000	Weak transcription	Spleen	Spleen
39	chr19:18870800-18876400	Enhancers	Esophagus	oesophagus
40	chr19:18870800-18876600	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr19:18871400-18874000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr19:18871400-18875200	Enhancers	Fetal Muscle Leg	muscle
43	chr19:18871600-18873200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr19:18871600-18873800	Enhancers	Fetal Brain Male	brain
45	chr19:18871800-18873200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr19:18871800-18873200	Enhancers	Stomach Mucosa	stomach
47	chr19:18871800-18873800	Genic enhancers	Fetal Intestine Small	intestine
48	chr19:18871800-18874000	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr19:18871800-18874600	Enhancers	Fetal Muscle Trunk	muscle
50	chr19:18871800-18874600	Enhancers	Gastric	stomach

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