Variant report

Variant	rs393195
Chromosome Location	chr19:44493142-44493143
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:44488273..44490047-chr19:44492744..44495947,3	MCF-7	breast:
2	chr19:44490423..44495330-chr19:44505190..44508106,4	K562	blood:
3	chr19:44491075..44493860-chr19:44504109..44508403,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000266921	Chromatin interaction
ENSG00000204920	Chromatin interaction
ENSG00000159882	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs370809	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs381091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs381628	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs381759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs381888	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs381983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs382255	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs391267	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs392889	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs393536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs395803	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs396116	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs396148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs396497	1.00[CEU][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs396786	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs397683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs402785	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs405763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs414402	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs419839	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs420355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs420584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs421505	1.00[CEU][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs431509	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs436739	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs436790	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs448692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469650	chr19:44405994-44555426	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv912109	chr19:44459074-44493142	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs393195	BCAT2	cis	cerebellum	SCAN
rs393195	KLK10	cis	parietal	SCAN
rs393195	SPIB	cis	parietal	SCAN
rs393195	FOXA3	cis	cerebellum	SCAN
rs393195	ZNF175	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44489000-44493600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr19:44489200-44493200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr19:44489200-44493200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr19:44489200-44493400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr19:44489200-44493400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr19:44489200-44493400	Weak transcription	Brain Angular Gyrus	brain
7	chr19:44489200-44493400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr19:44489200-44493600	Weak transcription	Colonic Mucosa	Colon
9	chr19:44489200-44494600	Weak transcription	Gastric	stomach
10	chr19:44489200-44494600	Weak transcription	NHLF	lung
11	chr19:44489200-44496000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr19:44489200-44496000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr19:44489200-44496000	Weak transcription	Small Intestine	intestine
14	chr19:44489200-44496600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr19:44489200-44500400	Weak transcription	HUVEC	blood vessel
16	chr19:44489200-44506200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr19:44489200-44506200	Weak transcription	Hela-S3	cervix
18	chr19:44489400-44493200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr19:44489400-44493200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr19:44489400-44493200	Weak transcription	Placenta	Placenta
21	chr19:44489400-44493200	Weak transcription	NHEK	skin
22	chr19:44489400-44493400	Weak transcription	Brain Anterior Caudate	brain
23	chr19:44489400-44493400	Weak transcription	NH-A	brain
24	chr19:44489400-44493600	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr19:44489400-44493600	Weak transcription	Primary B cells from cord blood	blood
26	chr19:44489400-44493600	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr19:44489400-44494000	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr19:44489400-44495600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr19:44489400-44496600	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr19:44489600-44493200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr19:44489600-44493400	Weak transcription	Osteobl	bone
32	chr19:44489600-44493600	Weak transcription	Esophagus	oesophagus
33	chr19:44489600-44494600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr19:44489600-44494800	Weak transcription	Fetal Intestine Small	intestine
35	chr19:44489600-44495600	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr19:44489600-44496000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr19:44489600-44496200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr19:44489600-44506200	Weak transcription	HepG2	liver
39	chr19:44490000-44493600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr19:44490000-44494800	Weak transcription	Spleen	Spleen
41	chr19:44490200-44493200	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr19:44490200-44493400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr19:44490200-44493400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr19:44490200-44493400	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr19:44490200-44493600	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr19:44490400-44494600	Weak transcription	Fetal Heart	heart
47	chr19:44491000-44494000	ZNF genes & repeats	GM12878-XiMat	blood
48	chr19:44491000-44500200	Strong transcription	Fetal Lung	lung
49	chr19:44491000-44501600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
50	chr19:44491000-44503400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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