Variant report

Variant	rs12608613
Chromosome Location	chr19:40029386-40029387
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39977704..39980525-chr19:40028766..40030427,2	K562	blood:
2	chr19:39923941..39928347-chr19:40027705..40030840,3	MCF-7	breast:
3	chr19:39901022..39904778-chr19:40029097..40032980,4	MCF-7	breast:
4	chr19:39925083..39928891-chr19:40028576..40030872,3	K562	blood:
5	chr19:39890843..39892874-chr19:40028629..40030722,2	MCF-7	breast:
6	chr19:39880332..39881919-chr19:40028970..40031203,2	K562	blood:
7	chr19:39959218..39961854-chr19:40028748..40031663,2	K562	blood:
8	chr19:40023614..40026391-chr19:40028689..40031990,5	MCF-7	breast:
9	chr19:40019907..40024445-chr19:40029285..40031709,4	MCF-7	breast:
10	chr19:40024943..40026873-chr19:40027805..40030767,4	MCF-7	breast:
11	chr19:39925003..39927867-chr19:40028857..40032200,4	K562	blood:
12	chr19:39923771..39928393-chr19:40029138..40032183,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000006712	Chromatin interaction
ENSG00000105197	Chromatin interaction
ENSG00000196235	Chromatin interaction
ENSG00000090924	Chromatin interaction
ENSG00000105193	Chromatin interaction
ENSG00000176401	Chromatin interaction
ENSG00000269584	Chromatin interaction
ENSG00000269792	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10439100	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1123301	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1368468	0.95[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.90[MEX][hapmap];0.96[MKK][hapmap];0.85[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1433106	0.87[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs1991831	0.87[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs4447549	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs4803255	0.89[ASN][1000 genomes]
rs6508867	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6508868	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7245901	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7246072	0.95[CEU][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8108097	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8110685	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]

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	nsv911690	chr19:39903088-40046863	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv911691	chr19:39979966-40029386	Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv911692	chr19:39979966-40046863	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv1060251	chr19:39982988-40099773	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
5	nsv911693	chr19:39986241-40033574	Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv579509	chr19:40004640-40133438	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
7	nsv911694	chr19:40015907-40031369	Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12608613	SLC8A2	cis	parietal	SCAN
rs12608613	C5AR1	cis	parietal	SCAN
rs12608613	NUMBL	cis	parietal	SCAN
rs12608613	KLC3	cis	cerebellum	SCAN
rs12608613	CABP5	cis	cerebellum	SCAN
rs12608613	BCL3	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40023600-40029800	Weak transcription	Aorta	Aorta
2	chr19:40023600-40029800	Weak transcription	Left Ventricle	heart
3	chr19:40024000-40029600	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr19:40024000-40029600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr19:40024000-40029600	Weak transcription	Fetal Stomach	stomach
6	chr19:40024000-40029800	Weak transcription	Colonic Mucosa	Colon
7	chr19:40024200-40029800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr19:40028200-40029400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr19:40028200-40029600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr19:40028400-40029400	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr19:40028400-40029400	Enhancers	Brain Anterior Caudate	brain
12	chr19:40028400-40029600	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr19:40028400-40029600	Enhancers	Brain Germinal Matrix	brain
14	chr19:40028400-40029600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr19:40028600-40029600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr19:40028600-40029600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr19:40028800-40029400	Enhancers	Primary T cells from cord blood	blood
18	chr19:40028800-40029600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr19:40028800-40029600	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr19:40028800-40029600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr19:40028800-40029600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr19:40028800-40029600	Enhancers	Liver	Liver
23	chr19:40028800-40029600	Enhancers	Brain Cingulate Gyrus	brain
24	chr19:40028800-40029600	Enhancers	Brain Hippocampus Middle	brain
25	chr19:40028800-40029600	Enhancers	Fetal Brain Male	brain
26	chr19:40028800-40029800	Enhancers	Brain Substantia Nigra	brain
27	chr19:40028800-40030200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr19:40029000-40029400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr19:40029000-40029400	Active TSS	iPS-20b Cell Line	embryonic stem cell
30	chr19:40029000-40029400	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr19:40029000-40029400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr19:40029000-40029400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr19:40029000-40029400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr19:40029000-40029400	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr19:40029000-40029400	Enhancers	HSMMtube	muscle
36	chr19:40029000-40029400	Enhancers	NH-A	brain
37	chr19:40029000-40029400	Enhancers	NHDF-Ad	bronchial
38	chr19:40029000-40029600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr19:40029000-40029600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr19:40029000-40029600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr19:40029000-40029600	Active TSS	Brain Inferior Temporal Lobe	brain
42	chr19:40029000-40029600	Enhancers	Colon Smooth Muscle	Colon
43	chr19:40029000-40029600	Enhancers	Duodenum Mucosa	Duodenum
44	chr19:40029000-40029600	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr19:40029000-40029600	Enhancers	Fetal Lung	lung
46	chr19:40029000-40029600	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr19:40029000-40029600	Enhancers	Stomach Smooth Muscle	stomach
48	chr19:40029000-40029600	Enhancers	Hela-S3	cervix
49	chr19:40029000-40029600	Enhancers	Monocytes-CD14+_RO01746	blood
50	chr19:40029000-40029600	Enhancers	Osteobl	bone

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