Variant report

Variant	rs1014394
Chromosome Location	chr1:179800985-179800986
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179794929..179797401-chr1:179800739..179802497,2	MCF-7	breast:
2	chr1:179799294..179801607-chr1:179806721..179809341,2	MCF-7	breast:
3	chr1:179799799..179801521-chr1:180102704..180104863,2	K562	blood:
4	chr1:179784306..179787242-chr1:179799622..179801715,2	MCF-7	breast:
5	chr1:179798950..179801590-chr1:179923163..179925286,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260360	Chromatin interaction
ENSG00000135837	Chromatin interaction
ENSG00000229407	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1148812	0.80[EUR][1000 genomes]
rs1148815	0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs1148817	0.97[EUR][1000 genomes]
rs1148820	0.86[ASN][1000 genomes]
rs1148821	0.86[ASN][1000 genomes]
rs12062383	0.84[TSI][hapmap]
rs1281378	0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs1281408	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs1281411	0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs1281413	0.84[EUR][1000 genomes]
rs1281429	0.83[EUR][1000 genomes]
rs1281430	0.83[EUR][1000 genomes]
rs1281432	0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs1298477	0.81[EUR][1000 genomes]
rs1299684	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1300068	0.81[CEU][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs2007148	0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs2245425	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs2249346	0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs2252288	0.82[ASN][1000 genomes]
rs2252384	0.82[ASN][1000 genomes]
rs2252388	0.82[ASN][1000 genomes]
rs2777912	0.82[ASN][1000 genomes]
rs2777913	0.89[GIH][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs2777914	0.92[GIH][hapmap];0.84[ASN][1000 genomes]
rs2777915	0.82[ASN][1000 genomes]
rs2794579	0.89[GIH][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs2794582	0.86[EUR][1000 genomes]
rs2794583	0.84[EUR][1000 genomes]
rs475434	0.85[EUR][1000 genomes]
rs479094	0.85[CEU][hapmap];0.89[EUR][1000 genomes]
rs480498	0.88[EUR][1000 genomes]
rs486906	0.82[EUR][1000 genomes]
rs502036	0.82[MEX][hapmap]
rs514421	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs518774	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs538512	0.81[EUR][1000 genomes]
rs553830	0.88[EUR][1000 genomes]
rs589780	0.82[EUR][1000 genomes]
rs605807	0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs644412	0.81[TSI][hapmap]

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	nsv1005808	chr1:179783922-179864710	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv1005051	chr1:179785643-179861950	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
4	nsv429947	chr1:179790518-179925104	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1014394	TDRD5	cis	parietal	SCAN
rs1014394	IER5	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179791000-179807200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:179793800-179808800	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr1:179794600-179804800	Weak transcription	Right Ventricle	heart
4	chr1:179794800-179809200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr1:179795200-179812400	Weak transcription	Left Ventricle	heart
6	chr1:179795200-179815200	Weak transcription	Ovary	ovary
7	chr1:179795400-179804600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr1:179795400-179804800	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr1:179795400-179805000	Weak transcription	Fetal Muscle Leg	muscle
10	chr1:179795400-179807600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:179795400-179815200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:179795600-179834200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:179797400-179805800	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr1:179797600-179810000	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr1:179798400-179802400	Weak transcription	Placenta	Placenta
16	chr1:179798400-179805800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:179799600-179815200	Weak transcription	Brain Angular Gyrus	brain
18	chr1:179799800-179801000	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr1:179799800-179801000	Enhancers	Thymus	Thymus
20	chr1:179799800-179801200	Enhancers	Primary T cells from cord blood	blood
21	chr1:179799800-179801200	Enhancers	Primary T cells fromperipheralblood	blood
22	chr1:179799800-179801200	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr1:179799800-179802600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr1:179799800-179802600	Enhancers	Fetal Thymus	thymus
25	chr1:179799800-179804800	Weak transcription	Adipose Nuclei	Adipose
26	chr1:179800000-179801000	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr1:179800000-179801000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr1:179800000-179801000	Enhancers	K562	blood
29	chr1:179800000-179801200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr1:179800000-179801800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr1:179800000-179801800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr1:179800200-179801000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr1:179800200-179801200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
34	chr1:179800200-179801200	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr1:179800400-179801000	Enhancers	HMEC	breast
36	chr1:179800400-179801200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr1:179800400-179801200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr1:179800400-179801400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
39	chr1:179800400-179801800	Flanking Active TSS	Dnd41	blood
40	chr1:179800400-179808800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr1:179800400-179809000	Weak transcription	Stomach Smooth Muscle	stomach
42	chr1:179800400-179815200	Weak transcription	Psoas Muscle	Psoas
43	chr1:179800600-179801200	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr1:179800600-179801200	Enhancers	Lung	lung
45	chr1:179800600-179801200	Enhancers	Spleen	Spleen
46	chr1:179800600-179801800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr1:179800600-179815200	Weak transcription	Esophagus	oesophagus
48	chr1:179800800-179801200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:179800800-179801200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr1:179800800-179801400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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