Variant report

Variant	rs757318
Chromosome Location	chr19:18820308-18820309
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	chr19:18805952..18808937-chr19:18819749..18821987,2	MCF-7	breast:
2	chr19:18818727..18820395-chr19:18861333..18863526,2	MCF-7	breast:

Extended variants
information (count: 15 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10404726	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11668971	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11878477	0.82[EUR][1000 genomes]
rs11880870	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808149	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808150	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808152	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808153	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808844	0.82[CEU][hapmap];0.83[GIH][hapmap]
rs7257332	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9304955	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs757318	ZNF738	cis	parietal	SCAN
rs757318	TMEM59L	cis	cerebellum	SCAN
rs757318	ANKLE1	cis	parietal	SCAN
rs757318	ZNF714	cis	parietal	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18797200-18822400	Weak transcription	HepG2	liver
2	chr19:18812000-18844200	Weak transcription	Fetal Kidney	kidney
3	chr19:18812200-18823600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr19:18812400-18820400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr19:18812400-18821000	Weak transcription	Fetal Lung	lung
6	chr19:18812400-18821800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr19:18812400-18821800	Weak transcription	Fetal Intestine Small	intestine
8	chr19:18812400-18824000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr19:18812400-18824000	Weak transcription	Fetal Brain Female	brain
10	chr19:18812400-18827600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr19:18812400-18827800	Weak transcription	Brain Germinal Matrix	brain
12	chr19:18812600-18821800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr19:18812600-18825800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr19:18812600-18828200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr19:18813400-18820800	Weak transcription	Primary B cells from cord blood	blood
16	chr19:18818000-18836600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr19:18818600-18822400	Enhancers	Primary T cells fromperipheralblood	blood
18	chr19:18818800-18821200	Enhancers	Lung	lung
19	chr19:18818800-18821200	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr19:18818800-18821400	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr19:18818800-18821800	Weak transcription	Colon Smooth Muscle	Colon
22	chr19:18818800-18823600	Enhancers	Fetal Muscle Trunk	muscle
23	chr19:18819000-18824000	Enhancers	Fetal Muscle Leg	muscle
24	chr19:18819000-18844000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr19:18819200-18821200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr19:18819400-18820400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr19:18819400-18820600	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr19:18819400-18821400	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr19:18819400-18821400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr19:18819600-18820400	Enhancers	Rectal Mucosa Donor 29	rectum
31	chr19:18819600-18820400	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr19:18819600-18820400	Enhancers	Stomach Smooth Muscle	stomach
33	chr19:18819600-18821200	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr19:18819600-18821200	Enhancers	Colonic Mucosa	Colon
35	chr19:18819600-18821400	Enhancers	Primary B cells from peripheral blood	blood
36	chr19:18819600-18821400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr19:18819600-18824400	Weak transcription	Aorta	Aorta
38	chr19:18819800-18820400	Enhancers	Brain Angular Gyrus	brain
39	chr19:18819800-18820400	Weak transcription	Esophagus	oesophagus
40	chr19:18819800-18820400	Enhancers	Fetal Thymus	thymus
41	chr19:18819800-18820800	Enhancers	Gastric	stomach
42	chr19:18819800-18821000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr19:18819800-18821200	Enhancers	Left Ventricle	heart
44	chr19:18819800-18822000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr19:18819800-18822600	Enhancers	Adipose Nuclei	Adipose
46	chr19:18819800-18823800	Weak transcription	Pancreas	Pancrea
47	chr19:18820000-18820400	Enhancers	Duodenum Mucosa	Duodenum
48	chr19:18820000-18820800	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr19:18820000-18821000	Weak transcription	Placenta	Placenta
50	chr19:18820000-18821200	Enhancers	Right Ventricle	heart

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