Variant report

Variant	rs752067
Chromosome Location	chr19:39142329-39142330
allele	C/T
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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39138022..39142840-chr19:39322070..39325450,5	MCF-7	breast:
2	chr19:39141235..39143219-chr19:39170803..39172948,2	K562	blood:
3	chr19:39141347..39144030-chr19:39208371..39211834,3	MCF-7	breast:
4	chr19:39109194..39111209-chr19:39140540..39143105,2	MCF-7	breast:
5	chr19:39140809..39143009-chr19:39198249..39199895,2	MCF-7	breast:
6	chr19:39142246..39144499-chr19:39217661..39220429,2	K562	blood:
7	chr19:39141727..39145361-chr19:39153035..39156463,3	K562	blood:
8	chr19:39137047..39143767-chr19:39341076..39344906,12	MCF-7	breast:
9	chr19:39141654..39143815-chr19:39327217..39328958,2	MCF-7	breast:
10	chr19:39138189..39142372-chr19:39210085..39214804,5	MCF-7	breast:
11	chr19:39136970..39140096-chr19:39140173..39145438,10	MCF-7	breast:
12	chr19:39140411..39144509-chr19:39172304..39176724,4	K562	blood:
13	chr19:39140553..39142565-chr19:39169330..39171049,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000130402	Chromatin interaction
ENSG00000178982	Chromatin interaction
ENSG00000104814	Chromatin interaction
ENSG00000104823	Chromatin interaction
ENSG00000104824	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1031849	0.92[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	0.97[CHD][hapmap];1.00[JPT][hapmap]
rs11665964	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12462503	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]
rs12976749	0.81[CHB][hapmap]
rs12984247	0.89[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.87[MEX][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1564203	0.94[ASW][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];0.81[ASN][1000 genomes]
rs1985636	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2080988	0.83[ASN][1000 genomes]
rs2112649	0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[ASN][1000 genomes]
rs2112651	0.87[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];0.83[GIH][hapmap];0.87[JPT][hapmap]
rs4802743	0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[ASN][1000 genomes]
rs6508813	0.89[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.87[MEX][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6508814	0.83[ASN][1000 genomes]
rs7252630	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[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]
rs755690	0.83[ASN][1000 genomes]
rs8099948	0.80[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[ASN][1000 genomes]
rs8107877	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs888996	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs888997	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9304576	0.89[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9304577	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs936524	0.81[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	nsv911667	chr19:39119898-39143289	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs752067	CTD-2540F13.2	cis	Nerve Tibial	GTEx
rs752067	CAPN12	cis	Adipose Subcutaneous	GTEx
rs752067	CAPN12	cis	Esophagus Muscularis	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39138200-39142600	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr19:39138600-39152200	Transcr. at gene 5' and 3'	A549	lung
3	chr19:39138800-39143800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr19:39139600-39143400	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
5	chr19:39139800-39143600	Flanking Active TSS	Duodenum Mucosa	Duodenum
6	chr19:39140000-39143400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr19:39140400-39142400	Flanking Active TSS	HUVEC	blood vessel
8	chr19:39140400-39146800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr19:39140600-39142600	Flanking Active TSS	Hela-S3	cervix
10	chr19:39140600-39143400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:39140600-39151000	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr19:39140800-39142400	Flanking Active TSS	NH-A	brain
13	chr19:39140800-39142800	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr19:39140800-39143400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr19:39140800-39145200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr19:39141000-39142400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr19:39141000-39144000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr19:39141200-39143000	Enhancers	Primary T cells fromperipheralblood	blood
19	chr19:39141200-39143000	Enhancers	Brain Hippocampus Middle	brain
20	chr19:39141200-39143200	Enhancers	Brain Germinal Matrix	brain
21	chr19:39141200-39143400	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr19:39141200-39143600	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr19:39141200-39143600	Enhancers	Ovary	ovary
24	chr19:39141200-39143600	Enhancers	Spleen	Spleen
25	chr19:39141200-39143600	Flanking Active TSS	HepG2	liver
26	chr19:39141200-39143800	Enhancers	Placenta	Placenta
27	chr19:39141200-39144400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr19:39141200-39144400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
29	chr19:39141200-39145600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr19:39141200-39147000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr19:39141200-39147600	Enhancers	Primary hematopoietic stem cells	blood
32	chr19:39141200-39148600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr19:39141200-39148800	Enhancers	Placenta Amnion	Placenta Amnion
34	chr19:39141200-39162800	Enhancers	Psoas Muscle	Psoas
35	chr19:39141400-39142800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr19:39141400-39142800	Enhancers	Colon Smooth Muscle	Colon
37	chr19:39141400-39143000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr19:39141400-39143000	Enhancers	Brain Substantia Nigra	brain
39	chr19:39141400-39143200	Genic enhancers	Dnd41	blood
40	chr19:39141400-39143400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr19:39141400-39143400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr19:39141400-39143600	Enhancers	Lung	lung
43	chr19:39141400-39143600	Enhancers	Pancreas	Pancrea
44	chr19:39141400-39143800	Enhancers	Fetal Muscle Trunk	muscle
45	chr19:39141400-39144400	Enhancers	Primary B cells from cord blood	blood
46	chr19:39141400-39145400	Enhancers	Fetal Kidney	kidney
47	chr19:39141400-39146000	Enhancers	Brain Anterior Caudate	brain
48	chr19:39141400-39146400	Enhancers	H1 Cell Line	embryonic stem cell
49	chr19:39141400-39147000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr19:39141400-39147800	Enhancers	Small Intestine	intestine

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