Variant report

Variant	rs1348161
Chromosome Location	chr4:102252696-102252697
allele	A/G
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	GATA2	chr4:102252519-102252792	SH-SY5Y	brain:	n/a	n/a
2	GATA3	chr4:102252483-102252842	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:102252145..102254033-chr4:102258356..102260817,2	MCF-7	breast:

Variant related genes	Relation type
MIR1255A	TF binding region

Extended variants
information (count: 87 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10007902	0.96[CEU][hapmap];0.86[JPT][hapmap]
rs10017730	0.80[EUR][1000 genomes]
rs1031033	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1031034	1.00[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1031035	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10433980	0.80[EUR][1000 genomes]
rs10433981	0.82[EUR][1000 genomes]
rs10433982	0.82[EUR][1000 genomes]
rs13109704	0.82[EUR][1000 genomes]
rs13135441	0.80[EUR][1000 genomes]
rs1441433	0.95[JPT][hapmap]
rs1476159	0.83[EUR][1000 genomes]
rs1530259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1549513	0.96[CEU][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap]
rs1549515	0.96[CEU][hapmap];0.89[JPT][hapmap]
rs1549516	0.96[CEU][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap]
rs1822168	0.80[EUR][1000 genomes]
rs1822169	0.80[EUR][1000 genomes]
rs2044043	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2583385	0.83[EUR][1000 genomes]
rs2583386	0.83[EUR][1000 genomes]
rs2583387	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2583389	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs2583391	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2583392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2583394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2583395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2583397	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2583398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2583399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2583400	0.90[JPT][hapmap]
rs2583401	0.86[JPT][hapmap]
rs2583402	0.81[JPT][hapmap]
rs2583406	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2850326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2850328	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2850329	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2850330	0.90[EUR][1000 genomes]
rs2850331	0.90[EUR][1000 genomes]
rs2850332	0.91[JPT][hapmap]
rs2850333	0.83[EUR][1000 genomes]
rs2850334	0.83[EUR][1000 genomes]
rs2850344	0.91[JPT][hapmap]
rs2850350	0.86[JPT][hapmap]
rs2850351	0.91[JPT][hapmap]
rs2850354	0.91[JPT][hapmap]
rs2850355	0.95[JPT][hapmap]
rs2850356	0.95[JPT][hapmap]
rs2850357	0.82[ASN][1000 genomes]
rs2850366	1.00[CEU][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2850367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2850368	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2850369	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.81[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2850370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2850371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2850372	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2850963	0.91[JPT][hapmap]
rs2850969	0.91[JPT][hapmap]
rs2850974	0.91[JPT][hapmap]
rs2850976	0.91[JPT][hapmap]
rs28664200	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4452435	0.96[CEU][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs4574415	0.83[EUR][1000 genomes]
rs4698957	0.80[EUR][1000 genomes]
rs4699209	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4699210	0.82[EUR][1000 genomes]
rs4699211	0.82[EUR][1000 genomes]
rs4699212	0.80[EUR][1000 genomes]
rs4699214	0.80[EUR][1000 genomes]
rs6532928	0.80[EUR][1000 genomes]
rs6816400	0.80[EUR][1000 genomes]
rs6824603	0.80[EUR][1000 genomes]
rs6845368	0.82[EUR][1000 genomes]
rs6846097	0.82[EUR][1000 genomes]
rs6852377	0.82[EUR][1000 genomes]
rs6856370	0.80[EUR][1000 genomes]
rs755961	0.91[JPT][hapmap]
rs7668224	0.82[EUR][1000 genomes]
rs7687487	0.82[EUR][1000 genomes]
rs920559	0.82[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931418	chr4:101500167-102443207	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv999741	chr4:102009017-102454115	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537199	chr4:102009017-102454115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1004766	chr4:102009017-102713765	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537200	chr4:102009017-102713765	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1011351	chr4:102056024-102450302	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
7	nsv879676	chr4:102202285-102340930	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1348161	FLJ20021	cis	multi-tissue	Pritchard
rs1348161	EIF4E	cis	cerebellum	SCAN
rs1348161	AP001816.1	cis	Whole Blood	GTEx

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102243400-102256000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr4:102243600-102256800	Weak transcription	Aorta	Aorta
3	chr4:102244000-102258000	Weak transcription	Brain Angular Gyrus	brain
4	chr4:102245600-102252800	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr4:102245600-102255000	Weak transcription	Ovary	ovary
6	chr4:102249600-102266400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr4:102249800-102256000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr4:102250000-102253200	Weak transcription	Primary B cells from cord blood	blood
9	chr4:102250200-102258200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr4:102250200-102265200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr4:102250400-102265800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr4:102250600-102255000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr4:102250600-102255800	Weak transcription	GM12878-XiMat	blood
14	chr4:102250600-102266000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr4:102250800-102255000	Weak transcription	Gastric	stomach
16	chr4:102251000-102256200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr4:102251000-102256200	Weak transcription	Liver	Liver
18	chr4:102251000-102256200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr4:102251000-102256400	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr4:102251000-102256400	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr4:102251000-102258200	Weak transcription	Dnd41	blood
22	chr4:102251000-102260200	Weak transcription	Brain Anterior Caudate	brain
23	chr4:102251200-102255800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr4:102251200-102255800	Weak transcription	Small Intestine	intestine
25	chr4:102251200-102256200	Weak transcription	Duodenum Mucosa	Duodenum
26	chr4:102251200-102258000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr4:102251200-102259600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr4:102251200-102265800	Weak transcription	Brain Hippocampus Middle	brain
29	chr4:102251400-102253000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr4:102251400-102256000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr4:102251600-102253200	Enhancers	HMEC	breast
32	chr4:102251600-102253400	Enhancers	NHEK	skin
33	chr4:102251600-102253600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr4:102251600-102255800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr4:102251800-102256000	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr4:102251800-102256000	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr4:102251800-102256400	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr4:102252000-102253200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr4:102252000-102253400	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr4:102252000-102253800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr4:102252000-102255800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr4:102252000-102256200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr4:102252000-102256200	Weak transcription	Adipose Nuclei	Adipose
44	chr4:102252000-102258000	Weak transcription	Primary T cells from cord blood	blood
45	chr4:102252000-102265800	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr4:102252200-102253800	Enhancers	Psoas Muscle	Psoas
47	chr4:102252200-102255400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr4:102252200-102256200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr4:102252200-102258400	Weak transcription	Osteobl	bone
50	chr4:102252200-102266000	Weak transcription	Fetal Lung	lung

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