Variant report

Variant	rs414402
Chromosome Location	chr19:44492568-44492569
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

Variant related genes	Relation type
ENSG00000266921	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];0.91[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs381091	1.00[ASW][hapmap];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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs381628	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs381759	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs381888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs381983	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs382255	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs391267	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs392889	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs393195	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]
rs393536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs395803	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs396116	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[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];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs396497	1.00[CEU][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs396786	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs397683	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs402785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs405763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs419839	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs420355	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs420584	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs421505	1.00[CEU][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs431509	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs436739	0.95[AMR][1000 genomes];0.99[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];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs448692	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[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
rs414402	BCAT2	cis	cerebellum	SCAN
rs414402	FOXA3	cis	cerebellum	SCAN
rs414402	SPIB	cis	parietal	SCAN
rs414402	KLK10	cis	parietal	SCAN
rs414402	ZNF175	cis	cerebellum	SCAN

Chromatin state (count:116 , 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	chr19:44489200-44492600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr19:44489200-44492600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr19:44489200-44492600	Weak transcription	Fetal Muscle Leg	muscle
5	chr19:44489200-44492600	Weak transcription	Psoas Muscle	Psoas
6	chr19:44489200-44493000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr19:44489200-44493200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr19:44489200-44493200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr19:44489200-44493400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr19:44489200-44493400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr19:44489200-44493400	Weak transcription	Brain Angular Gyrus	brain
12	chr19:44489200-44493400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr19:44489200-44493600	Weak transcription	Colonic Mucosa	Colon
14	chr19:44489200-44494600	Weak transcription	Gastric	stomach
15	chr19:44489200-44494600	Weak transcription	NHLF	lung
16	chr19:44489200-44496000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:44489200-44496000	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr19:44489200-44496000	Weak transcription	Small Intestine	intestine
19	chr19:44489200-44496600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr19:44489200-44500400	Weak transcription	HUVEC	blood vessel
21	chr19:44489200-44506200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr19:44489200-44506200	Weak transcription	Hela-S3	cervix
23	chr19:44489400-44492600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr19:44489400-44492600	Weak transcription	Brain Germinal Matrix	brain
25	chr19:44489400-44492600	Weak transcription	Duodenum Mucosa	Duodenum
26	chr19:44489400-44492600	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr19:44489400-44492600	Weak transcription	Stomach Smooth Muscle	stomach
28	chr19:44489400-44492600	Weak transcription	Thymus	Thymus
29	chr19:44489400-44492800	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr19:44489400-44492800	Weak transcription	Brain Substantia Nigra	brain
31	chr19:44489400-44492800	Weak transcription	Fetal Brain Female	brain
32	chr19:44489400-44492800	Weak transcription	Fetal Thymus	thymus
33	chr19:44489400-44492800	Weak transcription	NHDF-Ad	bronchial
34	chr19:44489400-44493000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr19:44489400-44493200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr19:44489400-44493200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr19:44489400-44493200	Weak transcription	Placenta	Placenta
38	chr19:44489400-44493200	Weak transcription	NHEK	skin
39	chr19:44489400-44493400	Weak transcription	Brain Anterior Caudate	brain
40	chr19:44489400-44493400	Weak transcription	NH-A	brain
41	chr19:44489400-44493600	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr19:44489400-44493600	Weak transcription	Primary B cells from cord blood	blood
43	chr19:44489400-44493600	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr19:44489400-44494000	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr19:44489400-44495600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr19:44489400-44496600	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr19:44489600-44492600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr19:44489600-44492600	Weak transcription	Primary B cells from peripheral blood	blood
49	chr19:44489600-44492600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr19:44489600-44492600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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