Variant report

Variant	rs4244330
Chromosome Location	chr10:99530851-99530852
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:99526747..99528824-chr10:99529529..99531423,2	MCF-7	breast:
2	chr10:99522811..99525043-chr10:99528774..99531185,2	K562	blood:

Extended variants
information (count: 68 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10748709	0.80[ASN][1000 genomes]
rs10786367	0.85[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.82[ASN][1000 genomes]
rs10786370	0.85[CEU][hapmap];0.82[JPT][hapmap];0.85[MEX][hapmap]
rs10786371	0.91[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.88[ASN][1000 genomes]
rs10786372	0.90[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs10786373	0.82[ASN][1000 genomes]
rs10786374	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10882993	0.80[CEU][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs10882995	0.94[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10882996	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10882997	0.83[EUR][1000 genomes]
rs11189350	0.85[ASN][1000 genomes]
rs11189352	0.86[ASN][1000 genomes]
rs11189353	0.80[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs11189355	0.94[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11189356	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11189357	0.94[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11189359	0.94[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11189360	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11189361	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11189362	1.00[CEU][hapmap];0.85[JPT][hapmap];0.87[EUR][1000 genomes]
rs11189367	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11189374	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11189376	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11189377	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11591898	0.89[ASN][1000 genomes]
rs11597378	0.94[CHB][hapmap]
rs12412543	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12569711	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12569757	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12780534	0.86[ASN][1000 genomes]
rs12783992	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1538723	0.89[ASN][1000 genomes]
rs1556971	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1981237	1.00[CEU][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs1981238	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2039826	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34283185	0.83[EUR][1000 genomes]
rs3750612	0.94[CEU][hapmap];0.83[JPT][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes]
rs3750614	0.80[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.89[ASN][1000 genomes]
rs3750615	0.85[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs3814558	0.80[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs3814559	1.00[CEU][hapmap];0.91[JPT][hapmap];0.88[EUR][1000 genomes]
rs3814560	1.00[CEU][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs4244329	1.00[CEU][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs4917784	0.90[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs4917785	0.83[ASN][1000 genomes]
rs4917786	0.82[AMR][1000 genomes]
rs4919139	0.83[CEU][hapmap];0.82[ASN][1000 genomes]
rs7080894	0.91[JPT][hapmap]
rs7080953	1.00[CEU][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7081361	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7081652	0.82[ASN][1000 genomes]
rs7099540	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7100453	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7478323	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7907679	0.85[CEU][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap]
rs7910589	0.80[ASN][1000 genomes]
rs7916164	0.87[EUR][1000 genomes]
rs7916454	0.80[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7922907	0.94[CEU][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs883324	0.85[CEU][hapmap];0.83[JPT][hapmap]
rs946777	0.80[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs946778	0.80[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	esv3340017	chr10:99530387-99533135	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4244330	ZFYVE27	cis	parietal	SCAN
rs4244330	ZFYVE27	cis	cerebellum	SCAN
rs4244330	DHDPSL	cis	cerebellum	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99526400-99531200	Weak transcription	K562	blood
2	chr10:99529600-99531400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
3	chr10:99530000-99531400	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
4	chr10:99530200-99531000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
5	chr10:99530200-99531200	Bivalent Enhancer	Fetal Thymus	thymus
6	chr10:99530200-99532200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
7	chr10:99530400-99531000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
8	chr10:99530400-99531000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
9	chr10:99530400-99531000	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr10:99530400-99531000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr10:99530400-99531000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr10:99530400-99531000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr10:99530400-99531000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr10:99530400-99531000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
15	chr10:99530400-99531200	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr10:99530400-99531400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
17	chr10:99530400-99531400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
18	chr10:99530400-99531400	Bivalent Enhancer	Fetal Brain Male	brain
19	chr10:99530400-99531400	Flanking Active TSS	Pancreas	Pancrea
20	chr10:99530400-99532200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
21	chr10:99530600-99531000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr10:99530600-99531000	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr10:99530600-99531000	Bivalent Enhancer	Primary B cells from cord blood	blood
24	chr10:99530600-99531000	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
25	chr10:99530600-99531000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr10:99530600-99531000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr10:99530600-99531000	Bivalent Enhancer	Fetal Heart	heart
28	chr10:99530600-99531000	Active TSS	Gastric	stomach
29	chr10:99530600-99531000	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
30	chr10:99530600-99531000	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
31	chr10:99530600-99531000	Flanking Bivalent TSS/Enh	A549	lung
32	chr10:99530600-99531200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
33	chr10:99530600-99531200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
34	chr10:99530600-99531200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
35	chr10:99530600-99531200	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
36	chr10:99530600-99531200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
37	chr10:99530600-99531200	Bivalent Enhancer	Fetal Muscle Leg	muscle
38	chr10:99530600-99531200	Bivalent Enhancer	Fetal Stomach	stomach
39	chr10:99530600-99531400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr10:99530600-99531400	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
41	chr10:99530600-99531400	Bivalent/Poised TSS	Primary T cells from cord blood	blood
42	chr10:99530600-99531400	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
43	chr10:99530600-99531400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr10:99530600-99531400	Bivalent/Poised TSS	Brain Anterior Caudate	brain
45	chr10:99530600-99531600	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
46	chr10:99530600-99531600	Bivalent/Poised TSS	HSMM	muscle
47	chr10:99530600-99532000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
48	chr10:99530600-99532000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
49	chr10:99530600-99532200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
50	chr10:99530600-99532200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell

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