Variant report

Variant	rs10220690
Chromosome Location	chr14:35076498-35076499
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	chr14:35075909..35077812-chr14:35078602..35081587,2	MCF-7	breast:
2	chr14:35074454..35077190-chr17:57969192..57971747,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108423	Chromatin interaction
ENSG00000108443	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10131004	0.90[ASN][1000 genomes]
rs10136826	0.93[ASW][hapmap];0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];0.86[TSI][hapmap];0.87[YRI][hapmap];0.95[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10151832	0.93[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];1.00[ASN][1000 genomes]
rs10872887	0.92[ASN][1000 genomes]
rs11156850	0.93[ASW][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];0.84[LWK][hapmap];0.84[MKK][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11620787	0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs12432069	0.86[CHB][hapmap]
rs12432539	0.93[ASW][hapmap];0.80[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];0.86[TSI][hapmap];0.86[YRI][hapmap];0.95[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12717240	0.92[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs12880885	0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];0.89[TSI][hapmap];0.90[ASN][1000 genomes]
rs12883317	0.86[ASW][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap]
rs12891984	0.97[ASN][1000 genomes]
rs28537636	0.95[ASN][1000 genomes]
rs34612921	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4258505	0.86[ASN][1000 genomes]
rs4304943	0.86[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap]
rs4403967	0.93[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4598814	0.93[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs4612970	0.90[ASN][1000 genomes]
rs4981244	0.86[ASW][hapmap];0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs55938117	0.95[ASN][1000 genomes]
rs60370017	0.95[ASN][1000 genomes]
rs7144882	0.97[ASN][1000 genomes]
rs7146283	1.00[ASW][hapmap];0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.89[TSI][hapmap];0.91[YRI][hapmap];0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7148910	0.90[ASN][1000 genomes]
rs7149128	0.82[ASN][1000 genomes]
rs7149200	0.93[ASW][hapmap];0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.89[TSI][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7151142	0.81[CHD][hapmap]
rs7151482	0.81[CHD][hapmap];0.88[GIH][hapmap]
rs7151774	1.00[ASW][hapmap];0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.89[TSI][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7153635	0.81[CHD][hapmap]
rs7154505	0.86[ASW][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap]
rs7155411	0.90[ASN][1000 genomes]
rs7158783	0.93[ASW][hapmap];0.80[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];0.84[LWK][hapmap];0.84[MKK][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs72675226	0.95[ASN][1000 genomes]
rs72675236	0.95[ASN][1000 genomes]
rs72675245	0.90[ASN][1000 genomes]
rs7493420	0.97[ASN][1000 genomes]
rs7493480	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs8008918	0.90[ASN][1000 genomes]
rs8018552	0.90[ASN][1000 genomes]
rs8018701	0.90[ASN][1000 genomes]
rs8018918	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040980	chr14:34345018-35255592	Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv1048408	chr14:34958352-35255592	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Genic 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	63 gene(s)	inside rSNPs	diseases
3	esv3392700	chr14:34989406-35365530	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	nsv1040303	chr14:35040853-35101044	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv542027	chr14:35040853-35101044	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv1038360	chr14:35040853-35152886	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	esv3408652	chr14:35069966-35110821	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv523334	chr14:35075022-35131862	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10220690	EAPP	cis	parietal	SCAN
rs10220690	FOXA1	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:35031400-35078000	Strong transcription	Primary B cells from peripheral blood	blood
2	chr14:35031600-35079400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr14:35032000-35078200	Strong transcription	Fetal Muscle Trunk	muscle
4	chr14:35032000-35078600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr14:35032200-35080600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr14:35033000-35079000	Strong transcription	HepG2	liver
7	chr14:35040600-35080400	Strong transcription	Duodenum Mucosa	Duodenum
8	chr14:35041600-35080200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr14:35045800-35079000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr14:35045800-35079400	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr14:35045800-35089200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr14:35046200-35078400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr14:35046200-35079600	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr14:35046400-35078400	Strong transcription	Dnd41	blood
15	chr14:35046600-35078400	Strong transcription	Fetal Intestine Large	intestine
16	chr14:35047200-35079400	Strong transcription	Placenta	Placenta
17	chr14:35048200-35079600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr14:35048400-35079000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr14:35048600-35077600	Strong transcription	Primary T cells from cord blood	blood
20	chr14:35048600-35079400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr14:35049000-35078200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr14:35050800-35078000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr14:35051800-35078400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr14:35053800-35082200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr14:35054600-35098400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr14:35056600-35078000	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr14:35056600-35079000	Strong transcription	Adipose Nuclei	Adipose
28	chr14:35056600-35079400	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr14:35057000-35079200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr14:35057200-35078200	Strong transcription	Fetal Muscle Leg	muscle
31	chr14:35057400-35077800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr14:35057400-35078000	Strong transcription	Stomach Smooth Muscle	stomach
33	chr14:35057400-35079400	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr14:35057400-35079400	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr14:35057400-35079600	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr14:35057400-35079600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr14:35057600-35079200	Strong transcription	Liver	Liver
38	chr14:35057600-35079600	Strong transcription	Fetal Thymus	thymus
39	chr14:35058400-35089200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr14:35058600-35077800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr14:35058800-35078400	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr14:35060000-35080400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr14:35060800-35097800	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr14:35063000-35098400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr14:35063200-35077600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr14:35063200-35077600	Strong transcription	Brain Hippocampus Middle	brain
47	chr14:35064400-35079200	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr14:35064600-35079200	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr14:35065600-35078000	Strong transcription	Brain Germinal Matrix	brain
50	chr14:35065600-35079400	Strong transcription	Duodenum Smooth Muscle	Duodenum

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