Variant report

Variant	rs12973480
Chromosome Location	chr19:18809694-18809695
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:18809327..18811934-chr19:18826162..18828018,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10409207	0.89[YRI][hapmap]
rs11665980	0.85[CEU][hapmap];1.00[GIH][hapmap]
rs11668413	0.85[CEU][hapmap];1.00[GIH][hapmap]
rs11670024	0.96[EUR][1000 genomes]
rs11670437	0.85[CEU][hapmap];1.00[GIH][hapmap]
rs12980791	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13344506	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17683623	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34931002	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35212572	0.93[EUR][1000 genomes]
rs3752217	0.80[CEU][hapmap]
rs3764628	0.85[CEU][hapmap];1.00[GIH][hapmap]
rs7253058	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8100814	0.89[YRI][hapmap]
rs8102070	0.82[AMR][1000 genomes];0.81[EUR][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	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	nsv911286	chr19:18652844-18811112	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv911289	chr19:18700047-18811112	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	esv3393439	chr19:18807352-18811750	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv960927	chr19:18808010-18837082	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12973480	SIGLEC7	trans	cerebellum	SCAN
rs12973480	USHBP1	cis	parietal	SCAN
rs12973480	EPS15L1	cis	parietal	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18795400-18810800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr19:18795400-18811400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr19:18795400-18811400	Weak transcription	NH-A	brain
4	chr19:18795600-18810000	Weak transcription	Thymus	Thymus
5	chr19:18795600-18810800	Weak transcription	Ovary	ovary
6	chr19:18795800-18809800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr19:18795800-18810600	Weak transcription	Brain Hippocampus Middle	brain
8	chr19:18795800-18810600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr19:18795800-18810800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr19:18795800-18811000	Weak transcription	Fetal Intestine Large	intestine
11	chr19:18795800-18811400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr19:18795800-18811400	Weak transcription	Fetal Lung	lung
13	chr19:18795800-18811400	Weak transcription	Right Atrium	heart
14	chr19:18796200-18810600	Weak transcription	Brain Anterior Caudate	brain
15	chr19:18796200-18811200	Weak transcription	Fetal Brain Female	brain
16	chr19:18796600-18810800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr19:18797200-18810600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr19:18797200-18811200	Weak transcription	NHLF	lung
19	chr19:18797200-18822400	Weak transcription	HepG2	liver
20	chr19:18797800-18809800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr19:18798400-18810800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr19:18799000-18810800	Weak transcription	Brain Germinal Matrix	brain
23	chr19:18799200-18810400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr19:18799200-18810800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr19:18803200-18811000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr19:18806200-18810600	Weak transcription	Fetal Brain Male	brain
27	chr19:18806600-18810600	Enhancers	Primary T cells fromperipheralblood	blood
28	chr19:18806800-18810200	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr19:18806800-18810400	Enhancers	Primary B cells from peripheral blood	blood
30	chr19:18807200-18810600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr19:18807400-18809800	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr19:18807600-18810200	Weak transcription	K562	blood
33	chr19:18807800-18809800	Enhancers	Right Ventricle	heart
34	chr19:18807800-18810400	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr19:18807800-18811000	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr19:18808000-18811600	Weak transcription	Fetal Kidney	kidney
37	chr19:18808000-18811600	Enhancers	Stomach Mucosa	stomach
38	chr19:18808200-18809800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr19:18808400-18810000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr19:18808400-18810000	Enhancers	Gastric	stomach
41	chr19:18808400-18810200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr19:18808400-18810400	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr19:18808400-18810400	Weak transcription	Liver	Liver
44	chr19:18808400-18810600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr19:18808400-18811000	Enhancers	Duodenum Mucosa	Duodenum
46	chr19:18808400-18811400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr19:18808400-18811400	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr19:18808600-18809800	Strong transcription	Fetal Intestine Small	intestine
49	chr19:18808600-18810000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr19:18808600-18810200	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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