Variant report

Variant	rs2237012
Chromosome Location	chr4:55599998-55599999
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	chr4:55594122..55596921-chr4:55598697..55601658,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000157404	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1124007	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11935331	1.00[CEU][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17084694	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17084702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17084716	1.00[CEU][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17084733	1.00[CEU][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2237014	0.96[ASN][1000 genomes]
rs2276949	1.00[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2298976	0.91[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3733542	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3796776	0.89[ASN][1000 genomes]
rs3822214	1.00[CEU][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73234238	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8022	0.91[CEU][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[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	nsv999400	chr4:55143598-55776995	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	esv3367952	chr4:55437113-55724644	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv526344	chr4:55522488-56231119	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2237012	SRP72	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:55561000-55606600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr4:55576400-55602000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr4:55576400-55602600	Weak transcription	Fetal Muscle Leg	muscle
4	chr4:55584400-55606200	Weak transcription	Brain Hippocampus Middle	brain
5	chr4:55585200-55608400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr4:55586600-55604600	Weak transcription	Lung	lung
7	chr4:55587800-55607600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr4:55588200-55608000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr4:55588600-55611600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr4:55589600-55608400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr4:55589800-55607400	Weak transcription	Left Ventricle	heart
12	chr4:55590000-55603400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr4:55590000-55608000	Strong transcription	Primary hematopoietic stem cells	blood
14	chr4:55590600-55602200	Weak transcription	Fetal Brain Female	brain
15	chr4:55592600-55609000	Weak transcription	Fetal Stomach	stomach
16	chr4:55593400-55607200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr4:55593600-55602600	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr4:55593600-55606800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr4:55593800-55600400	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr4:55594200-55602200	Weak transcription	Aorta	Aorta
21	chr4:55594400-55602600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr4:55594400-55607000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr4:55597000-55600600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr4:55597800-55603000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr4:55597800-55603200	Weak transcription	Ovary	ovary
26	chr4:55597800-55607600	Weak transcription	Fetal Kidney	kidney
27	chr4:55598000-55603200	Weak transcription	Fetal Muscle Trunk	muscle
28	chr4:55598200-55600000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:55598200-55601600	Weak transcription	NHDF-Ad	bronchial
30	chr4:55598200-55607400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr4:55599200-55600800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr4:55599400-55601000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr4:55599600-55602600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr4:55599800-55602000	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr4:55599800-55602200	Weak transcription	HUES64 Cell Line	embryonic stem cell

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