Variant report

Variant	rs946778
Chromosome Location	chr10:99509457-99509458
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:99509146-99509509	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:99496988..99498940-chr10:99509067..99511500,2	MCF-7	breast:
2	chr10:99495273..99496977-chr10:99508285..99510585,2	MCF-7	breast:
3	chr10:99503209..99504783-chr10:99507206..99509576,2	MCF-7	breast:
4	chr10:99495471..99497724-chr10:99507676..99509768,2	MCF-7	breast:

Variant related genes	Relation type
ZFYVE27	TF binding region
ENSG00000155256	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10786367	0.95[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10786370	0.95[CEU][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap]
rs10786371	0.94[ASW][hapmap];0.95[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];0.98[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10786372	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10882993	1.00[CEU][hapmap];0.82[CHD][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.81[EUR][1000 genomes]
rs10882994	0.83[EUR][1000 genomes]
rs10882995	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10882996	0.93[ASN][1000 genomes]
rs11189350	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11189352	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11189353	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11189355	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11189356	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11189357	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11189359	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.97[ASN][1000 genomes]
rs11189360	0.80[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs11189361	0.83[ASN][1000 genomes]
rs11189367	0.88[ASN][1000 genomes]
rs11189374	0.86[ASN][1000 genomes]
rs11189376	0.86[ASN][1000 genomes]
rs11189377	0.85[ASN][1000 genomes]
rs11591898	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11597378	0.94[CHB][hapmap]
rs12412543	0.93[ASN][1000 genomes]
rs12569711	0.93[ASN][1000 genomes]
rs12569757	0.85[ASN][1000 genomes]
rs1538723	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1981237	0.80[CEU][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap]
rs1981238	0.80[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs2027376	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2039826	0.80[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.89[ASN][1000 genomes]
rs3750612	0.85[CEU][hapmap];0.82[CHD][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs3750614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3750615	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3814558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3814559	0.86[JPT][hapmap]
rs3814560	0.80[CEU][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap]
rs4244329	0.80[CEU][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap]
rs4244330	0.89[ASN][1000 genomes]
rs4917784	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs4917785	0.93[ASN][1000 genomes]
rs7080894	0.84[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs7080953	0.82[CHD][hapmap];0.85[JPT][hapmap]
rs7081361	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7099540	0.80[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7100453	0.86[ASN][1000 genomes]
rs7478323	0.89[ASN][1000 genomes]
rs7907679	0.95[CEU][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap]
rs7916454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7916593	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7922907	0.85[CEU][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs883324	0.95[CEU][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs946777	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1817777	chr10:99196035-99558169	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv467441	chr10:99472710-99541104	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv552026	chr10:99472710-99541104	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs946778	ZFYVE27	cis	parietal	SCAN
rs946778	MARVELD1	cis	lung	GTEx
rs946778	ZFYVE27	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99497600-99522600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr10:99498200-99520600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr10:99498400-99514800	Strong transcription	Fetal Stomach	stomach
4	chr10:99498400-99517600	Strong transcription	H1 Cell Line	embryonic stem cell
5	chr10:99498400-99519000	Strong transcription	Fetal Intestine Large	intestine
6	chr10:99498400-99519200	Strong transcription	Fetal Muscle Trunk	muscle
7	chr10:99498600-99514800	Strong transcription	Fetal Muscle Leg	muscle
8	chr10:99498600-99517800	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr10:99498600-99518000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr10:99498600-99518000	Strong transcription	Fetal Thymus	thymus
11	chr10:99498600-99520200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr10:99498600-99520600	Strong transcription	Osteobl	bone
13	chr10:99498600-99522200	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr10:99498600-99522400	Strong transcription	Duodenum Mucosa	Duodenum
15	chr10:99498600-99522400	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr10:99498600-99523000	Strong transcription	Thymus	Thymus
17	chr10:99498600-99523600	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr10:99498600-99524800	Weak transcription	Fetal Brain Male	brain
19	chr10:99498800-99522400	Strong transcription	Dnd41	blood
20	chr10:99499000-99509600	Weak transcription	Psoas Muscle	Psoas
21	chr10:99499000-99517800	Strong transcription	Skeletal Muscle Female	skeletal muscle
22	chr10:99499000-99518000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr10:99499200-99517000	Strong transcription	HSMM	muscle
24	chr10:99499200-99518000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr10:99499200-99522800	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr10:99499200-99523400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr10:99499400-99519000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr10:99499400-99522000	Strong transcription	Stomach Smooth Muscle	stomach
29	chr10:99499400-99522400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr10:99499600-99519200	Strong transcription	Placenta	Placenta
31	chr10:99499800-99518000	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr10:99500000-99523000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr10:99500200-99518000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr10:99500400-99522000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr10:99500600-99523200	Strong transcription	Brain Germinal Matrix	brain
36	chr10:99500800-99517800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr10:99500800-99518800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr10:99501200-99517600	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr10:99501800-99517000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr10:99502000-99513200	Strong transcription	NHDF-Ad	bronchial
41	chr10:99502000-99517200	Strong transcription	HepG2	liver
42	chr10:99502000-99517600	Strong transcription	Rectal Smooth Muscle	rectum
43	chr10:99502000-99517800	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr10:99502000-99517800	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr10:99502000-99518000	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr10:99502000-99522800	Strong transcription	Primary B cells from peripheral blood	blood
47	chr10:99502200-99522600	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr10:99502400-99520000	Strong transcription	Primary B cells from cord blood	blood
49	chr10:99502600-99515800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr10:99502600-99517800	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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