Variant report

Variant	rs12462503
Chromosome Location	chr19:39152004-39152005
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39150052..39153067-chr19:39197622..39201361,3	MCF-7	breast:
2	chr19:39151862..39154243-chr19:39220891..39223454,2	MCF-7	breast:
3	chr19:39150956..39153225-chr19:39190082..39192763,2	MCF-7	breast:
4	chr19:39151900..39153408-chr19:39203433..39205156,2	MCF-7	breast:
5	chr19:39145586..39147740-chr19:39150423..39154465,3	K562	blood:
6	chr19:39150082..39153309-chr19:39178166..39180062,3	MCF-7	breast:
7	chr19:39149024..39154711-chr19:39158901..39163144,7	MCF-7	breast:
8	chr19:39151502..39153525-chr19:39175124..39177403,2	MCF-7	breast:
9	chr19:39151359..39154098-chr19:39320807..39323487,3	MCF-7	breast:
10	chr19:39151274..39153019-chr19:39209216..39212183,2	MCF-7	breast:
11	chr19:39150654..39152913-chr19:39172186..39173857,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000130402	Chromatin interaction
ENSG00000104823	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1031849	0.96[YRI][hapmap];0.81[ASN][1000 genomes]
rs10421863	0.80[CHB][hapmap];0.87[CHD][hapmap]
rs10424568	0.91[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1060186	0.83[ASW][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs11665964	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12976749	0.81[CHB][hapmap]
rs12984247	0.94[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.87[MEX][hapmap];0.98[MKK][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1564203	0.88[ASW][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];0.89[YRI][hapmap];0.81[ASN][1000 genomes]
rs1985636	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2080988	0.83[ASN][1000 genomes]
rs2112649	0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.83[ASN][1000 genomes]
rs2112651	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3786841	0.82[ASN][1000 genomes]
rs3786843	0.81[ASN][1000 genomes]
rs4347742	0.83[ASN][1000 genomes]
rs4801861	0.92[CHD][hapmap];0.80[GIH][hapmap];0.87[JPT][hapmap]
rs4802743	0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.83[ASN][1000 genomes]
rs6508813	0.94[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6508814	0.83[ASN][1000 genomes]
rs7252630	0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[ASN][1000 genomes]
rs749701	0.85[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs752067	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs755690	0.83[ASN][1000 genomes]
rs8099948	0.80[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[ASN][1000 genomes]
rs8107877	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs888996	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs888997	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9304576	0.94[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9304577	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs936524	0.81[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]

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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs12462503	CTD-2540F13.2	cis	Nerve Tibial	GTEx
rs12462503	RPS16	cis	parietal	SCAN
rs12462503	CCDC8	cis	parietal	SCAN
rs12462503	CAPN12	cis	Adipose Subcutaneous	GTEx
rs12462503	MEGF8	cis	cerebellum	SCAN
rs12462503	ERCC1	cis	cerebellum	SCAN
rs12462503	CAPN12	cis	multi-tissue	Pritchard
rs12462503	CAPN12	cis	lymphoblastoid	seeQTL
rs12462503	PSG3	cis	parietal	SCAN
rs12462503	PSG8	cis	parietal	SCAN
rs12462503	PPP1R13L	cis	cerebellum	SCAN
rs12462503	CAPN12	cis	Esophagus Muscularis	GTEx
rs12462503	LGALS17A	cis	cerebellum	SCAN

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	chr19:39141200-39162800	Enhancers	Psoas Muscle	Psoas
3	chr19:39143400-39154400	Enhancers	Brain Inferior Temporal Lobe	brain
4	chr19:39143800-39153200	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr19:39144200-39153400	Genic enhancers	K562	blood
6	chr19:39144400-39152200	Enhancers	Right Ventricle	heart
7	chr19:39144600-39154000	Enhancers	Right Atrium	heart
8	chr19:39144800-39154000	Genic enhancers	Fetal Intestine Large	intestine
9	chr19:39145200-39153400	Genic enhancers	Fetal Intestine Small	intestine
10	chr19:39147400-39160000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr19:39147600-39154000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr19:39147600-39154000	Enhancers	Brain Angular Gyrus	brain
13	chr19:39147800-39160800	Enhancers	Placenta	Placenta
14	chr19:39148000-39152800	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr19:39148600-39153400	Genic enhancers	HUES6 Cell Line	embryonic stem cell
16	chr19:39148800-39153000	Weak transcription	Primary B cells from cord blood	blood
17	chr19:39149000-39154200	Enhancers	Brain Substantia Nigra	brain
18	chr19:39149000-39154600	Weak transcription	Primary T cells from cord blood	blood
19	chr19:39149000-39155200	Weak transcription	Fetal Brain Female	brain
20	chr19:39149200-39153400	Genic enhancers	Fetal Muscle Leg	muscle
21	chr19:39149400-39152600	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr19:39149600-39152200	Enhancers	Ovary	ovary
23	chr19:39149600-39153200	Weak transcription	Brain Germinal Matrix	brain
24	chr19:39149600-39154000	Enhancers	Brain Hippocampus Middle	brain
25	chr19:39149600-39160200	Enhancers	Pancreas	Pancrea
26	chr19:39149800-39152200	Enhancers	Placenta Amnion	Placenta Amnion
27	chr19:39150000-39153000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr19:39150000-39157600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
29	chr19:39150200-39152800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr19:39150200-39152800	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr19:39150200-39154200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr19:39150400-39152600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr19:39150400-39152600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr19:39150400-39153200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr19:39150400-39153600	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr19:39150400-39154400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr19:39150400-39155000	Genic enhancers	HMEC	breast
38	chr19:39150600-39152600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr19:39150600-39153000	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr19:39150600-39154600	Genic enhancers	Osteobl	bone
41	chr19:39150800-39152200	Strong transcription	Primary B cells from peripheral blood	blood
42	chr19:39150800-39154400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr19:39150800-39155000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr19:39151000-39152200	Genic enhancers	Fetal Muscle Trunk	muscle
45	chr19:39151000-39152600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr19:39151000-39154400	Genic enhancers	Muscle Satellite Cultured Cells	--
47	chr19:39151000-39154600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr19:39151200-39152200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr19:39151200-39152200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr19:39151200-39153000	Genic enhancers	Stomach Smooth Muscle	stomach

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