Variant report

Variant	rs16972024
Chromosome Location	chr19:37645458-37645459
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	chr17:65989010..65991714-chr19:37644378..37646681,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000186665	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1047333	0.86[CHB][hapmap]
rs11667146	0.86[CHB][hapmap]
rs1657510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16972020	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16972028	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16972030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17304779	0.90[CHD][hapmap];0.83[GIH][hapmap]
rs1879497	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs2972598	0.81[CHD][hapmap]
rs3745768	0.86[CHB][hapmap]
rs3745770	0.86[CHB][hapmap]
rs4635449	0.89[ASN][1000 genomes]
rs58932518	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58973869	0.97[ASN][1000 genomes]
rs59892552	0.97[ASN][1000 genomes]
rs61448820	0.97[ASN][1000 genomes]
rs61733481	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73622753	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8108727	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers 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	61 gene(s)	inside rSNPs	diseases
4	nsv529817	chr19:36930549-37654062	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	nsv2477	chr19:37617348-37662207	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
15	esv3433517	chr19:37643755-37675928	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37613800-37662200	ZNF genes & repeats	Liver	Liver
2	chr19:37634400-37657800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr19:37635000-37656200	ZNF genes & repeats	Fetal Brain Female	brain
4	chr19:37635200-37661400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
5	chr19:37635200-37661600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:37637400-37656800	ZNF genes & repeats	Brain Anterior Caudate	brain
7	chr19:37639400-37663200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr19:37640400-37648000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr19:37640400-37659000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
10	chr19:37642000-37646000	Weak transcription	Pancreas	Pancrea
11	chr19:37642200-37646200	Weak transcription	Fetal Thymus	thymus
12	chr19:37643000-37650000	ZNF genes & repeats	Brain Germinal Matrix	brain
13	chr19:37643000-37661400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
14	chr19:37643000-37662000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr19:37643200-37645600	ZNF genes & repeats	Primary T killer memory cells from peripheral blood	blood
16	chr19:37643200-37646800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr19:37643200-37646800	ZNF genes & repeats	Right Ventricle	heart
18	chr19:37643200-37647800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
19	chr19:37643200-37649600	ZNF genes & repeats	Rectal Smooth Muscle	rectum
20	chr19:37643200-37650000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
21	chr19:37643200-37651000	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr19:37643200-37651200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
23	chr19:37643200-37651200	ZNF genes & repeats	Brain Substantia Nigra	brain
24	chr19:37643200-37654000	ZNF genes & repeats	Ovary	ovary
25	chr19:37643200-37654000	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
26	chr19:37643200-37654400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
27	chr19:37643200-37656800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr19:37643200-37658200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr19:37643200-37660800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
30	chr19:37643200-37661400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr19:37643200-37662400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr19:37643400-37645600	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr19:37643400-37645600	Strong transcription	Placenta	Placenta
34	chr19:37643400-37645800	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr19:37643400-37645800	ZNF genes & repeats	Fetal Lung	lung
36	chr19:37643400-37647000	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
37	chr19:37643400-37647200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
38	chr19:37643400-37647400	ZNF genes & repeats	Aorta	Aorta
39	chr19:37643400-37647600	ZNF genes & repeats	Brain Angular Gyrus	brain
40	chr19:37643400-37648000	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
41	chr19:37643400-37648400	ZNF genes & repeats	Fetal Muscle Trunk	muscle
42	chr19:37643400-37648600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
43	chr19:37643400-37648600	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
44	chr19:37643400-37649400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr19:37643400-37649400	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
46	chr19:37643400-37649600	ZNF genes & repeats	Fetal Muscle Leg	muscle
47	chr19:37643400-37651200	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
48	chr19:37643400-37651200	ZNF genes & repeats	Stomach Smooth Muscle	stomach
49	chr19:37643400-37652400	ZNF genes & repeats	Dnd41	blood
50	chr19:37643400-37653800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain

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