Variant report

Variant	rs4621106
Chromosome Location	chr19:19840768-19840769
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:19837998..19841957-chr19:19842344..19844108,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105708	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11669303	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12608993	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1979263	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2013571	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3207975	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71338402	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7246866	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7256487	0.81[JPT][hapmap]
rs7256992	0.81[JPT][hapmap]
rs7257691	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7259055	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8099910	0.81[JPT][hapmap]
rs8110890	1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs8112048	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer 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	67 gene(s)	inside rSNPs	diseases
3	esv3330851	chr19:19755507-19852881	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1065704	chr19:19797999-19865818	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv543929	chr19:19797999-19865818	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1062017	chr19:19803482-19865818	Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv543930	chr19:19803482-19865818	Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv1057601	chr19:19803482-19873623	ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv1063535	chr19:19806386-19863631	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv1062212	chr19:19806386-19869332	Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv1060122	chr19:19814678-19879575	Bivalent Enhancer ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv2436	chr19:19815858-19869171	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv911311	chr19:19831544-19863284	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	esv3318427	chr19:19833252-19841650	ZNF genes & repeats Weak transcription Genic enhancers Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv578791	chr19:19833627-19840768	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv436259	chr19:19833686-19840914	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	esv3376479	chr19:19833702-19840800	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4621106	ZNF14	cis	cerebellum	SCAN
rs4621106	ZNF14	cis	parietal	SCAN
rs4621106	ZNF43	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19828400-19843200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr19:19831000-19842600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr19:19831200-19843000	Weak transcription	NH-A	brain
4	chr19:19833200-19842600	Weak transcription	HSMM	muscle
5	chr19:19833400-19842400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr19:19835200-19841200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr19:19836400-19842600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr19:19836600-19842800	Weak transcription	Osteobl	bone
9	chr19:19836800-19841800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr19:19836800-19842400	ZNF genes & repeats	Fetal Muscle Leg	muscle
11	chr19:19837000-19841800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr19:19837000-19842400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr19:19837000-19842600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
14	chr19:19837200-19841400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
15	chr19:19837200-19842800	ZNF genes & repeats	Fetal Intestine Small	intestine
16	chr19:19837400-19841000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
17	chr19:19837400-19841200	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
18	chr19:19837400-19841400	ZNF genes & repeats	Brain Anterior Caudate	brain
19	chr19:19837400-19842400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
20	chr19:19837400-19842800	ZNF genes & repeats	Fetal Brain Female	brain
21	chr19:19837600-19841000	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
22	chr19:19837600-19841200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr19:19837600-19841200	ZNF genes & repeats	Brain Cingulate Gyrus	brain
24	chr19:19837600-19841400	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
25	chr19:19837600-19841400	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
26	chr19:19837600-19841600	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
27	chr19:19837600-19842200	ZNF genes & repeats	Dnd41	blood
28	chr19:19837600-19842400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr19:19837600-19842400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
30	chr19:19837600-19842400	ZNF genes & repeats	Fetal Muscle Trunk	muscle
31	chr19:19837600-19842600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
32	chr19:19837800-19840800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
33	chr19:19837800-19840800	ZNF genes & repeats	Adipose Nuclei	Adipose
34	chr19:19837800-19840800	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
35	chr19:19837800-19841000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
36	chr19:19837800-19841000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
37	chr19:19837800-19841200	ZNF genes & repeats	Thymus	Thymus
38	chr19:19837800-19841400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
39	chr19:19837800-19842200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr19:19837800-19842200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
41	chr19:19837800-19842800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr19:19838000-19842200	ZNF genes & repeats	Primary T cells from cord blood	blood
43	chr19:19838000-19842800	ZNF genes & repeats	Brain Germinal Matrix	brain
44	chr19:19838200-19841400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr19:19838200-19841400	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr19:19838200-19842400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr19:19838400-19840800	ZNF genes & repeats	HepG2	liver
48	chr19:19838400-19841000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
49	chr19:19838400-19842600	Weak transcription	Pancreas	Pancrea
50	chr19:19838600-19842400	ZNF genes & repeats	Fetal Intestine Large	intestine

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