Variant report

Variant	rs604127
Chromosome Location	chr2:31521289-31521290
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	chr2:31457063..31459277-chr2:31520684..31522523,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000013016	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11683836	1.00[JPT][hapmap]
rs12988379	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4951977	1.00[JPT][hapmap]
rs590009	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs604986	1.00[JPT][hapmap]
rs635092	0.87[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	nsv948552	chr2:31118599-31595424	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv949028	chr2:31502801-31665108	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
3	esv2762446	chr2:31521093-31610311	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs604127	IFT172	cis	parietal	SCAN
rs604127	UCN	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:31509200-31522000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr2:31511200-31523200	Weak transcription	HMEC	breast
3	chr2:31516200-31521600	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr2:31517200-31522200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr2:31517400-31522200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr2:31517600-31522600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:31517600-31523200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:31517800-31523200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr2:31517800-31523200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:31518600-31521400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:31518800-31521400	Enhancers	HSMMtube	muscle
12	chr2:31518800-31522600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:31518800-31523400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr2:31518800-31523800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr2:31519000-31521400	Enhancers	NH-A	brain
16	chr2:31519800-31523200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr2:31520000-31522200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr2:31520200-31521400	Enhancers	Primary B cells from peripheral blood	blood
19	chr2:31520200-31525000	Weak transcription	Fetal Lung	lung
20	chr2:31520400-31521400	Enhancers	Fetal Heart	heart
21	chr2:31520400-31525800	Weak transcription	Fetal Muscle Trunk	muscle
22	chr2:31520600-31525000	Weak transcription	Esophagus	oesophagus
23	chr2:31520600-31525800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr2:31520600-31526000	Weak transcription	Lung	lung
25	chr2:31520800-31521400	Enhancers	Placenta Amnion	Placenta Amnion
26	chr2:31521000-31521400	Enhancers	Primary B cells from cord blood	blood
27	chr2:31521000-31522200	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr2:31521000-31523000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr2:31521000-31523400	Weak transcription	NHEK	skin
30	chr2:31521000-31523800	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr2:31521000-31526400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr2:31521000-31526400	Weak transcription	Right Ventricle	heart
33	chr2:31521000-31527200	Weak transcription	Aorta	Aorta
34	chr2:31521200-31523400	Weak transcription	NHLF	lung
35	chr2:31521200-31525000	Weak transcription	Left Ventricle	heart

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