Variant report

Variant	rs10417966
Chromosome Location	chr19:57018082-57018083
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10404464	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10406271	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10406513	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10406535	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10406985	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10408108	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10414817	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10415223	0.88[EUR][1000 genomes]
rs10416884	0.88[EUR][1000 genomes]
rs10419553	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10419939	0.86[EUR][1000 genomes]
rs12973457	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12978999	0.82[LWK][hapmap]
rs12981768	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12981980	0.82[LWK][hapmap];0.80[YRI][hapmap]
rs12982001	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12984487	0.88[EUR][1000 genomes]
rs16987295	0.80[YRI][hapmap]
rs16987310	0.82[LWK][hapmap];0.80[YRI][hapmap]
rs17144	0.86[EUR][1000 genomes]
rs17273442	0.87[EUR][1000 genomes]
rs2058132	0.88[EUR][1000 genomes]
rs2189698	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286423	0.82[EUR][1000 genomes]
rs35780595	0.88[EUR][1000 genomes]
rs3752176	0.86[EUR][1000 genomes]
rs8106788	0.86[EUR][1000 genomes]
rs8110306	0.80[YRI][hapmap]
rs917407	0.80[YRI][hapmap]
rs958338	0.87[EUR][1000 genomes]
rs960995	0.86[EUR][1000 genomes]
rs993510	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949121	chr19:56754719-57591038	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1062341	chr19:56794070-57273332	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv544094	chr19:56794070-57273332	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
4	nsv1056713	chr19:56799151-57265682	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
5	nsv544095	chr19:56799151-57265682	Strong transcription ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Active 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	88 gene(s)	inside rSNPs	diseases
6	nsv580385	chr19:56918598-57072433	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv1057240	chr19:56919831-57153659	Flanking Active TSS Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv544097	chr19:56919831-57153659	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv580386	chr19:56924761-57072433	Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	nsv1055357	chr19:56933632-57190007	ZNF genes & repeats Strong transcription Active TSS Enhancers Weak transcription Flanking 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	26 gene(s)	inside rSNPs	diseases
11	nsv912518	chr19:56995737-57109821	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription 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	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10417966	ZFP28	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:57003000-57018800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:57003200-57018400	Weak transcription	Osteobl	bone
3	chr19:57006200-57018600	Weak transcription	Dnd41	blood
4	chr19:57007200-57018400	Weak transcription	HSMMtube	muscle
5	chr19:57007200-57018600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr19:57007600-57018600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr19:57007600-57018600	Weak transcription	Fetal Brain Male	brain
8	chr19:57007800-57018600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr19:57007800-57018600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr19:57007800-57018600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr19:57007800-57018600	Weak transcription	Brain Germinal Matrix	brain
12	chr19:57007800-57018600	Weak transcription	Esophagus	oesophagus
13	chr19:57007800-57018600	Weak transcription	Fetal Kidney	kidney
14	chr19:57007800-57018600	Weak transcription	Fetal Muscle Leg	muscle
15	chr19:57007800-57018600	Weak transcription	Left Ventricle	heart
16	chr19:57007800-57018600	Weak transcription	Right Ventricle	heart
17	chr19:57007800-57019200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr19:57008000-57018400	Weak transcription	Fetal Brain Female	brain
19	chr19:57008400-57018600	Weak transcription	Fetal Stomach	stomach
20	chr19:57008600-57018600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr19:57009000-57018200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr19:57009600-57018200	Weak transcription	Brain Anterior Caudate	brain
23	chr19:57009800-57018400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr19:57009800-57018400	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr19:57010000-57018600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr19:57011800-57018600	Weak transcription	Rectal Smooth Muscle	rectum
27	chr19:57012400-57018400	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr19:57012600-57018600	Weak transcription	Fetal Muscle Trunk	muscle
29	chr19:57013200-57018400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr19:57013600-57018400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr19:57014400-57018400	Weak transcription	Brain Angular Gyrus	brain
32	chr19:57014600-57018400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr19:57014600-57018400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr19:57014600-57018600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr19:57014600-57018600	Weak transcription	Ovary	ovary
36	chr19:57014600-57018600	Weak transcription	Pancreas	Pancrea
37	chr19:57014800-57018400	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr19:57016600-57018200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr19:57016600-57018600	Weak transcription	HSMM	muscle
40	chr19:57017200-57018400	ZNF genes & repeats	Liver	Liver
41	chr19:57017200-57019000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
42	chr19:57017800-57018200	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr19:57018000-57018400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
44	chr19:57018000-57018600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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