Variant report

Variant	rs454376
Chromosome Location	chr19:44435167-44435168
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:44433359..44436193-chr19:44439011..44441074,2	MCF-7	breast:
2	chr19:44423954..44427054-chr19:44433272..44435317,3	K562	blood:
3	chr19:44431244..44433244-chr19:44435117..44436858,2	MCF-7	breast:
4	chr19:44422838..44425972-chr19:44433802..44436613,3	K562	blood:

Variant related genes	Relation type
ENSG00000124459	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10402944	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2299936	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2429734	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs364278	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs366431	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs368492	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs376655	0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs377931	0.83[GIH][hapmap]
rs377934	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs381220	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs381872	0.82[GIH][hapmap]
rs385202	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs385578	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs386249	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs386747	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs387504	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs388547	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs390134	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs391961	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs394132	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs394380	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs395419	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs396188	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs400591	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs401770	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs413061	0.89[GIH][hapmap];0.85[AMR][1000 genomes]
rs415867	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs418336	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs424041	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs427401	0.85[AMR][1000 genomes]
rs429611	0.85[AMR][1000 genomes]
rs437700	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs439417	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs441386	0.85[AMR][1000 genomes]
rs441742	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs442543	0.84[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs444816	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs445865	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs453682	1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912108	chr19:44358761-44435167	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	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
3	nsv579854	chr19:44411543-44490024	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs454376	KLC3	cis	parietal	SCAN
rs454376	ZNF155	Cis_1M	lymphoblastoid	RTeQTL
rs454376	CYTH2	cis	parietal	SCAN
rs454376	ZNF155	cis	lymphoblastoid	seeQTL
rs454376	ZNF175	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44417000-44437400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr19:44418600-44437400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr19:44419400-44438600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr19:44420000-44437200	Strong transcription	Placenta	Placenta
5	chr19:44420000-44437400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr19:44420000-44437800	Strong transcription	HSMM	muscle
7	chr19:44420200-44437200	Strong transcription	HSMMtube	muscle
8	chr19:44420200-44437400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr19:44420400-44437400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr19:44420400-44438600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr19:44420600-44437000	Strong transcription	Dnd41	blood
12	chr19:44420600-44437200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr19:44420600-44437200	Strong transcription	Fetal Thymus	thymus
14	chr19:44420600-44437400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr19:44420600-44437600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr19:44420800-44436200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr19:44420800-44437600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr19:44421000-44437000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr19:44421000-44437000	Strong transcription	Brain Anterior Caudate	brain
20	chr19:44421000-44437200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr19:44421000-44437400	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr19:44421000-44438200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr19:44421000-44438200	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr19:44421200-44437400	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr19:44421400-44437200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr19:44421400-44437600	Strong transcription	Brain Substantia Nigra	brain
27	chr19:44422000-44437000	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr19:44422400-44437200	Strong transcription	Brain Angular Gyrus	brain
29	chr19:44422600-44437400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr19:44422800-44437400	Strong transcription	Fetal Muscle Trunk	muscle
31	chr19:44423200-44437000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr19:44423600-44437000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr19:44423800-44437200	Strong transcription	Brain Inferior Temporal Lobe	brain
34	chr19:44423800-44437400	Strong transcription	Primary B cells from peripheral blood	blood
35	chr19:44424000-44436800	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr19:44424000-44436800	Strong transcription	NH-A	brain
37	chr19:44424000-44437200	Strong transcription	Duodenum Mucosa	Duodenum
38	chr19:44424000-44438600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr19:44424400-44437600	Strong transcription	Fetal Muscle Leg	muscle
40	chr19:44425000-44437400	Strong transcription	Fetal Intestine Large	intestine
41	chr19:44425000-44437400	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr19:44425200-44437400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr19:44425200-44437400	Strong transcription	Brain Germinal Matrix	brain
44	chr19:44425400-44437200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr19:44425400-44437400	Strong transcription	Primary B cells from cord blood	blood
46	chr19:44425400-44437600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr19:44425800-44437000	Strong transcription	Primary T cells from cord blood	blood
48	chr19:44426000-44437000	Strong transcription	Fetal Brain Female	brain
49	chr19:44426000-44437400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr19:44426200-44437000	Strong transcription	Brain Hippocampus Middle	brain

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