Variant report

Variant	rs12610472
Chromosome Location	chr19:44564401-44564402
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:44563861..44566757-chr19:44575129..44577196,2	MCF-7	breast:
2	chr19:44561763..44564477-chr19:44574561..44577058,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000186026	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11083734	0.83[ASN][1000 genomes]
rs11083735	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11083736	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11083737	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666432	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1474061	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1996409	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2138823	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2138824	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2176431	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35120085	0.83[ASN][1000 genomes]
rs382197	0.86[EUR][1000 genomes]
rs3826941	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4239528	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs427608	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4299256	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4371266	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4375771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4444434	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs451388	0.92[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes]
rs454904	0.92[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4550576	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4555257	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4580302	0.82[ASN][1000 genomes]
rs4803668	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4803672	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4803674	0.85[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55798868	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56003307	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56230322	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56250154	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57895932	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62115491	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62119177	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6509135	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6509137	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6509139	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7251015	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7252213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7255192	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7257809	0.92[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8105003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8109313	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8109615	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8110348	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9646633	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833840	chr19:44520620-44715760	Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs12610472	C19orf73	cis	cerebellum	SCAN
rs12610472	ZNF223	cis	Adipose Subcutaneous	GTEx
rs12610472	ASPDH	cis	cerebellum	SCAN
rs12610472	CLPTM1	cis	cerebellum	SCAN
rs12610472	FUT2	cis	parietal	SCAN
rs12610472	ZNF223	cis	Nerve Tibial	GTEx
rs12610472	OPA3	cis	parietal	SCAN
rs12610472	APOE	cis	parietal	SCAN
rs12610472	ZNF223	cis	Thyroid	GTEx
rs12610472	KPTN	cis	parietal	SCAN
rs12610472	HIF3A	cis	parietal	SCAN
rs12610472	SNORD34	cis	parietal	SCAN
rs12610472	ETFB	cis	parietal	SCAN
rs12610472	ZNF223	cis	Skin Sun Exposed Lower leg	GTEx
rs12610472	ZNF613	cis	parietal	SCAN
rs12610472	ZNF223	cis	lung	GTEx
rs12610472	EMP3	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44556600-44564600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr19:44557000-44565000	Weak transcription	Psoas Muscle	Psoas
3	chr19:44557000-44566800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:44557000-44567400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr19:44557000-44567400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr19:44557000-44567600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr19:44557000-44568800	Weak transcription	HMEC	breast
8	chr19:44557000-44570200	Weak transcription	HUVEC	blood vessel
9	chr19:44557000-44570200	Weak transcription	NHDF-Ad	bronchial
10	chr19:44557000-44575600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr19:44557200-44565600	Weak transcription	NHLF	lung
12	chr19:44557400-44565000	Weak transcription	Small Intestine	intestine
13	chr19:44557400-44565000	Weak transcription	NH-A	brain
14	chr19:44557400-44570000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr19:44557400-44570200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr19:44557600-44564800	Weak transcription	Fetal Brain Male	brain
17	chr19:44558200-44571800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr19:44558200-44573200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr19:44558200-44575600	ZNF genes & repeats	Liver	Liver
20	chr19:44558800-44567800	Strong transcription	Stomach Smooth Muscle	stomach
21	chr19:44558800-44572800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
22	chr19:44559000-44565200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
23	chr19:44559200-44569000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr19:44559200-44569000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr19:44559200-44569400	Strong transcription	Fetal Stomach	stomach
26	chr19:44559400-44565400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr19:44559400-44565800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr19:44559400-44569400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr19:44559400-44570000	Weak transcription	Stomach Mucosa	stomach
30	chr19:44559600-44565800	Strong transcription	Colonic Mucosa	Colon
31	chr19:44559800-44568600	Strong transcription	HSMMtube	muscle
32	chr19:44560000-44568800	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr19:44560200-44567200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr19:44560400-44564600	Weak transcription	Primary B cells from cord blood	blood
35	chr19:44560400-44564600	Weak transcription	Primary B cells from peripheral blood	blood
36	chr19:44560400-44566400	Weak transcription	Fetal Thymus	thymus
37	chr19:44560400-44566800	Weak transcription	NHEK	skin
38	chr19:44560800-44569400	Strong transcription	Fetal Intestine Large	intestine
39	chr19:44560800-44570000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr19:44561000-44568800	Strong transcription	Fetal Brain Female	brain
41	chr19:44561000-44569200	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr19:44561200-44569600	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr19:44561400-44568400	Strong transcription	Brain Angular Gyrus	brain
44	chr19:44561400-44568800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr19:44561400-44569000	Strong transcription	Fetal Muscle Trunk	muscle
46	chr19:44561400-44570000	Strong transcription	Brain Hippocampus Middle	brain
47	chr19:44561600-44566000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr19:44561600-44567400	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr19:44561600-44568800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr19:44561600-44569000	Strong transcription	Brain Inferior Temporal Lobe	brain

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