Variant report

Variant	rs870046
Chromosome Location	chr1:180922807-180922808
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:180921716..180926405-chr1:180990463..180993659,6	MCF-7	breast:
2	chr1:180922049..180926985-chr1:181056376..181059811,8	MCF-7	breast:
3	chr1:180920141..180924832-chr1:180927695..180934337,6	MCF-7	breast:
4	chr1:180921700..180925041-chr1:180990802..180993603,10	MCF-7	breast:
5	chr1:180922269..180924346-chr1:181056350..181059480,3	MCF-7	breast:
6	chr1:180894020..180896970-chr1:180921543..180923993,2	MCF-7	breast:
7	chr1:180921489..180923428-chr1:180979617..180981443,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162783	Chromatin interaction
ENSG00000251520	Chromatin interaction
ENSG00000135823	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11799738	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2068800	0.80[MEX][hapmap]
rs2297184	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3820313	0.95[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs4651080	0.87[GIH][hapmap];0.83[MEX][hapmap]
rs4652540	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652542	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71630288	0.87[EUR][1000 genomes];0.93[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	nsv1014404	chr1:180770155-181090200	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv872579	chr1:180881148-180931508	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv2754938	chr1:180919343-180934343	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs870046	IER5	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180905400-180940600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:180911600-180928400	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr1:180911800-180927600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:180918000-180930000	Weak transcription	HSMMtube	muscle
5	chr1:180918400-180929000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr1:180918400-180929800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr1:180918400-180930000	Weak transcription	Hela-S3	cervix
8	chr1:180918600-180939800	Weak transcription	K562	blood
9	chr1:180918600-180944800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:180919000-180925000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr1:180919600-180923600	Weak transcription	Fetal Kidney	kidney
12	chr1:180919800-180928800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr1:180919800-180935800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:180920200-180923800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:180920200-180929000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr1:180920400-180923200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:180920600-180923200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:180920600-180923600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:180920800-180923000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:180920800-180923600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:180921200-180923000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:180921400-180926600	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr1:180921600-180923000	Enhancers	Fetal Heart	heart
24	chr1:180921800-180923000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr1:180921800-180923600	Enhancers	H1 Cell Line	embryonic stem cell
26	chr1:180922000-180923200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:180922200-180928200	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr1:180922200-180929200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr1:180922400-180923000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
30	chr1:180922400-180923000	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr1:180922400-180923000	Flanking Active TSS	GM12878-XiMat	blood
32	chr1:180922400-180923200	Flanking Active TSS	Stomach Smooth Muscle	stomach
33	chr1:180922400-180923800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:180922400-180923800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr1:180922400-180924000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
36	chr1:180922400-180924000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:180922400-180926800	Enhancers	Fetal Brain Male	brain
38	chr1:180922600-180923000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:180922600-180923000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
40	chr1:180922600-180923000	Flanking Active TSS	Primary B cells from peripheral blood	blood
41	chr1:180922600-180923000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
42	chr1:180922600-180923000	Flanking Active TSS	Primary hematopoietic stem cells	blood
43	chr1:180922600-180923000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
44	chr1:180922600-180923000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:180922600-180923000	Flanking Active TSS	Brain Angular Gyrus	brain
46	chr1:180922600-180923000	Flanking Active TSS	Brain Germinal Matrix	brain
47	chr1:180922600-180923000	Flanking Active TSS	Brain Hippocampus Middle	brain
48	chr1:180922600-180923000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
49	chr1:180922600-180923000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr1:180922600-180923000	Flanking Active TSS	Duodenum Mucosa	Duodenum

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