Variant report

Variant	rs2235797
Chromosome Location	chr1:210464758-210464759
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:210463032..210465736-chr1:210546022..210548079,2	MCF-7	breast:
2	chr1:210463570..210465979-chr1:210545857..210548788,4	MCF-7	breast:
3	chr1:210462820..210467272-chr1:210545539..210548914,4	K562	blood:
4	chr1:210405780..210407667-chr1:210464265..210465852,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000203706	Chromatin interaction
ENSG00000200972	Chromatin interaction
ENSG00000082497	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12123877	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12739013	0.84[GIH][hapmap];0.82[TSI][hapmap]
rs4314881	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs656753	0.84[GIH][hapmap];0.82[TSI][hapmap]
rs6666540	0.80[CEU][hapmap];0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv8769	chr1:210403509-210564588	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2235797	PFKFB2	cis	cerebellum	SCAN
rs2235797	SERTAD4	cis	parietal	SCAN
rs2235797	HHAT	cis	parietal	SCAN
rs2235797	SLC30A1	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210461800-210464800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:210462400-210464800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:210464200-210464800	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:210464200-210465000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:210464200-210465200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:210464200-210465600	Enhancers	Fetal Stomach	stomach
7	chr1:210464200-210467400	Enhancers	Fetal Lung	lung
8	chr1:210464400-210465200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:210464400-210465400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:210464400-210465400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
11	chr1:210464400-210465400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:210464400-210465400	Enhancers	Fetal Muscle Leg	muscle
13	chr1:210464400-210465400	Enhancers	Placenta	Placenta
14	chr1:210464600-210464800	Enhancers	Pancreatic Islets	Pancreatic Islet
15	chr1:210464600-210465000	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:210464600-210465200	Bivalent Enhancer	NH-A	brain
17	chr1:210464600-210465400	Enhancers	Adipose Nuclei	Adipose
18	chr1:210464600-210465600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr1:210464600-210466000	Enhancers	NHDF-Ad	bronchial
20	chr1:210464600-210466200	Enhancers	Fetal Heart	heart

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