Variant report

Variant	rs10406862
Chromosome Location	chr19:36519765-36519766
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:36515922..36517591-chr19:36519314..36521673,2	K562	blood:
2	chr19:36518073..36521044-chr19:36525057..36527255,2	K562	blood:
3	chr19:36499646..36502624-chr19:36517798..36521500,4	MCF-7	breast:
4	chr19:36512890..36520143-chr19:36521963..36527491,9	K562	blood:
5	chr19:36518180..36521030-chr19:36528618..36530229,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000181392	Chromatin interaction
ENSG00000105270	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1009381	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[ASN][1000 genomes]
rs10418079	0.85[YRI][hapmap]
rs10419924	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10420345	0.86[ASN][1000 genomes]
rs10421377	0.92[ASN][1000 genomes]
rs10422055	0.82[ASW][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.84[ASN][1000 genomes]
rs10425700	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.88[LWK][hapmap];0.93[MEX][hapmap];0.95[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10427033	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11538454	0.88[ASN][1000 genomes]
rs11666192	0.81[ASN][1000 genomes]
rs11669890	0.92[CHB][hapmap];0.96[CHD][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs12462159	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap]
rs12608517	0.82[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12981698	1.00[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap]
rs2023866	0.87[ASN][1000 genomes]
rs2074435	1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.82[ASN][1000 genomes]
rs2075472	0.93[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs2227260	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2231568	0.92[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap]
rs2301734	1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs2301737	1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs2871649	0.91[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4555271	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.88[LWK][hapmap];0.93[MEX][hapmap];0.95[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4806249	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4806254	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4806262	0.86[ASN][1000 genomes]
rs4806271	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4806273	0.82[ASN][1000 genomes]
rs4806276	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55849299	0.90[ASN][1000 genomes]
rs6510516	0.89[YRI][hapmap]
rs7250364	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7251912	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7257026	0.90[ASN][1000 genomes]
rs7258807	0.82[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73036134	0.80[ASN][1000 genomes]
rs8112640	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv911638	chr19:36265508-36537959	Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
4	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
5	esv1831737	chr19:36324324-36690874	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv911641	chr19:36473677-36536938	Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10406862	ZNF420	cis	cerebellum	SCAN
rs10406862	PHLDB3	cis	parietal	SCAN
rs10406862	ZNF527	cis	cerebellum	SCAN
rs10406862	MEGF8	cis	cerebellum	SCAN
rs10406862	POLR2I	cis	multi-tissue	Pritchard
rs10406862	PHLDB3	cis	cerebellum	SCAN
rs10406862	CYP2A7	cis	parietal	SCAN
rs10406862	WDR62	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36505600-36521000	Weak transcription	Fetal Brain Male	brain
2	chr19:36505800-36522000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr19:36505800-36522200	Weak transcription	Fetal Kidney	kidney
4	chr19:36505800-36522800	Weak transcription	Small Intestine	intestine
5	chr19:36506000-36522400	Weak transcription	NH-A	brain
6	chr19:36506000-36522800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr19:36506000-36523000	Weak transcription	HSMM	muscle
8	chr19:36506000-36523200	Weak transcription	Left Ventricle	heart
9	chr19:36506000-36523600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr19:36506200-36522400	Strong transcription	Fetal Stomach	stomach
11	chr19:36506200-36522800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr19:36506200-36523000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr19:36506200-36523200	Weak transcription	HUVEC	blood vessel
14	chr19:36506200-36523400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr19:36506200-36523400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr19:36506400-36519800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr19:36506400-36519800	Strong transcription	Stomach Smooth Muscle	stomach
18	chr19:36506400-36520400	Strong transcription	Brain Germinal Matrix	brain
19	chr19:36506400-36521600	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr19:36506400-36521800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr19:36506400-36523000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr19:36506400-36544400	Weak transcription	GM12878-XiMat	blood
23	chr19:36506800-36519800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr19:36506800-36532400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr19:36507000-36532200	Weak transcription	Hela-S3	cervix
26	chr19:36507600-36521800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr19:36507800-36519800	Strong transcription	Fetal Intestine Small	intestine
28	chr19:36508800-36519800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr19:36508800-36532400	Weak transcription	NHEK	skin
30	chr19:36511400-36519800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr19:36511400-36519800	Strong transcription	Fetal Muscle Trunk	muscle
32	chr19:36511400-36521800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr19:36511800-36519800	Strong transcription	Ovary	ovary
34	chr19:36513000-36519800	Strong transcription	Muscle Satellite Cultured Cells	--
35	chr19:36513400-36523600	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr19:36513600-36523000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr19:36513600-36525600	Weak transcription	K562	blood
38	chr19:36514400-36522400	Weak transcription	Liver	Liver
39	chr19:36514400-36523200	Weak transcription	Primary B cells from peripheral blood	blood
40	chr19:36514600-36519800	Strong transcription	Aorta	Aorta
41	chr19:36514600-36519800	Strong transcription	NHLF	lung
42	chr19:36515000-36522800	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr19:36515000-36523200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr19:36515200-36522800	Weak transcription	NHDF-Ad	bronchial
45	chr19:36515200-36523000	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr19:36515200-36527600	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr19:36515400-36523000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr19:36515400-36523200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr19:36515400-36523200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr19:36515400-36523600	Weak transcription	Skeletal Muscle Female	skeletal muscle

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