Variant report

Variant	rs3121310
Chromosome Location	chr1:228224824-228224825
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228206015..228208384-chr1:228223171..228225438,2	K562	blood:
2	chr1:228197639..228199875-chr1:228224226..228226074,2	K562	blood:
3	chr1:228222291..228225840-chr1:228229698..228232365,4	MCF-7	breast:
4	chr1:228223566..228226544-chr1:228251359..228253705,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10916265	0.86[YRI][hapmap]
rs1745417	0.83[YRI][hapmap]
rs1745423	0.80[TSI][hapmap]
rs1771467	0.82[YRI][hapmap]
rs28634124	0.90[EUR][1000 genomes]
rs3094911	0.89[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs3094912	0.83[YRI][hapmap]
rs3121309	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs697762	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs708111	0.82[YRI][hapmap]
rs708112	0.83[YRI][hapmap]
rs708113	0.83[CHB][hapmap];0.84[JPT][hapmap];0.90[YRI][hapmap]
rs708118	0.89[CHB][hapmap];0.89[CHD][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs708124	0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs752107	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs7523917	1.00[CEU][hapmap];0.89[GIH][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs766972	1.00[CEU][hapmap];0.86[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs822725	1.00[CEU][hapmap];0.89[GIH][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs822739	0.88[EUR][1000 genomes]
rs822740	0.88[EUR][1000 genomes]
rs849749	1.00[CEU][hapmap];0.89[GIH][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
5	nsv516409	chr1:228035131-228296745	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
7	nsv832803	chr1:228155118-228313681	Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
9	nsv945349	chr1:228186556-228245135	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3121310	ITPKB	cis	cerebellum	SCAN
rs3121310	OBSCN	cis	Esophagus Mucosa	GTEx
rs3121310	OBSCN	cis	Skin Sun Exposed Lower leg	GTEx
rs3121310	TMEM63A	cis	cerebellum	SCAN
rs3121310	ACBD3	cis	cerebellum	SCAN
rs3121310	WDR26	cis	cerebellum	SCAN
rs3121310	GUK1	cis	parietal	SCAN
rs3121310	C1orf69	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228219800-228225400	Weak transcription	Right Atrium	heart
2	chr1:228220000-228225200	Weak transcription	Esophagus	oesophagus
3	chr1:228222600-228225000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:228223000-228226600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:228223800-228225000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:228223800-228225200	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:228223800-228225400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
8	chr1:228223800-228225400	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:228224000-228225400	Bivalent Enhancer	Fetal Lung	lung
10	chr1:228224400-228226000	Bivalent Enhancer	Lung	lung
11	chr1:228224600-228225000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:228224800-228225000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
13	chr1:228224800-228225000	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:228224800-228225200	Weak transcription	Fetal Heart	heart
15	chr1:228224800-228225400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:228224800-228225400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin

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