Variant report

Variant	rs11667417
Chromosome Location	chr19:37726119-37726120
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:37708605..37710654-chr19:37725265..37728083,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188283	Chromatin interaction
ENSG00000245680	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11673185	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11673646	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12459637	0.94[EUR][1000 genomes]
rs2385372	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic 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 miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv3507199	chr19:37284708-37805639	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv3507200	chr19:37284708-37805639	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv3497360	chr19:37290273-37745365	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription 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 miRNA target site	25 gene(s)	inside rSNPs	diseases
5	esv3497361	chr19:37290273-37745365	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv458568	chr19:37325826-37747108	Strong transcription ZNF genes & repeats Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv579461	chr19:37325826-37747108	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv911652	chr19:37437106-37774299	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv911654	chr19:37487632-37758082	Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS 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 miRNA target site	16 gene(s)	inside rSNPs	diseases
10	nsv911655	chr19:37646745-37758082	ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Weak 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	13 gene(s)	inside rSNPs	diseases
11	nsv961287	chr19:37708789-37742224	ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	n/a
12	nsv960833	chr19:37715348-37733416	Strong transcription ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
13	nsv9717	chr19:37721760-37796698	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11667417	AC012309.5	cis	Thyroid	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37710000-37728600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:37710200-37728600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr19:37710400-37744200	ZNF genes & repeats	Liver	Liver
4	chr19:37711000-37737000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr19:37711000-37737800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:37711200-37738200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
7	chr19:37713400-37728400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr19:37715200-37736600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
9	chr19:37715200-37740400	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
10	chr19:37715400-37732600	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
11	chr19:37715400-37738400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
12	chr19:37715600-37727000	Strong transcription	Placenta	Placenta
13	chr19:37715600-37736000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
14	chr19:37715800-37738000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
15	chr19:37716000-37736000	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
16	chr19:37716200-37731600	Strong transcription	Brain Germinal Matrix	brain
17	chr19:37718400-37735600	ZNF genes & repeats	Primary T cells from cord blood	blood
18	chr19:37718400-37735600	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
19	chr19:37719000-37726400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr19:37719600-37726600	Strong transcription	Skeletal Muscle Male	skeletal muscle
21	chr19:37720800-37727400	ZNF genes & repeats	Fetal Lung	lung
22	chr19:37720800-37735400	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
23	chr19:37720800-37735400	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
24	chr19:37720800-37736200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
25	chr19:37720800-37736400	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
26	chr19:37720800-37738600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
27	chr19:37720800-37740200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr19:37720800-37740400	ZNF genes & repeats	Adipose Nuclei	Adipose
29	chr19:37721400-37726200	Weak transcription	Rectal Smooth Muscle	rectum
30	chr19:37721400-37726400	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr19:37721400-37726400	Weak transcription	Stomach Mucosa	stomach
32	chr19:37721800-37726400	Weak transcription	Brain Cingulate Gyrus	brain
33	chr19:37722000-37726400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr19:37722000-37726400	Weak transcription	NH-A	brain
35	chr19:37722000-37726600	Weak transcription	HUVEC	blood vessel
36	chr19:37722600-37737800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr19:37722800-37726200	Weak transcription	Brain Angular Gyrus	brain
38	chr19:37722800-37726200	Weak transcription	Hela-S3	cervix
39	chr19:37723200-37729200	Strong transcription	Osteobl	bone
40	chr19:37723800-37726200	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr19:37723800-37727000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr19:37724000-37726200	Weak transcription	Fetal Kidney	kidney
43	chr19:37724000-37726200	Weak transcription	NHDF-Ad	bronchial
44	chr19:37724000-37737000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr19:37724200-37726200	ZNF genes & repeats	Fetal Stomach	stomach
46	chr19:37724200-37727000	ZNF genes & repeats	Pancreas	Pancrea
47	chr19:37724200-37732600	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
48	chr19:37724200-37737000	ZNF genes & repeats	Ovary	ovary
49	chr19:37724400-37726200	Weak transcription	Stomach Smooth Muscle	stomach
50	chr19:37724400-37732400	ZNF genes & repeats	Fetal Intestine Small	intestine

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