Variant report

Variant	rs637871
Chromosome Location	chr12:50287592-50287593
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50133876..50136071-chr12:50286990..50288779,2	MCF-7	breast:
2	chr12:50286408..50287924-chr12:50296514..50298335,2	MCF-7	breast:
3	chr12:50285473..50288081-chr12:50312540..50314584,2	K562	blood:
4	chr12:50281662..50285882-chr12:50286690..50289422,5	MCF-7	breast:
5	chr12:50286993..50289592-chr12:50396016..50398113,2	MCF-7	breast:
6	chr12:50285846..50288716-chr12:50291928..50294510,3	K562	blood:

Variant related genes	Relation type
ENSG00000161800	Chromatin interaction
ENSG00000139644	Chromatin interaction
ENSG00000135472	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs417644	0.92[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs422022	0.81[EUR][1000 genomes]
rs608233	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs611282	0.91[CEU][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs612674	1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs632151	0.92[CEU][hapmap]
rs836964	0.92[CEU][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv522972	chr12:50196394-50410831	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
5	nsv832407	chr12:50243268-50412236	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv558835	chr12:50275137-50433234	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	nsv525920	chr12:50285061-50304949	Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs637871	C1QL4	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50267000-50297000	Weak transcription	Right Atrium	heart
2	chr12:50275000-50294800	Weak transcription	Fetal Brain Male	brain
3	chr12:50277800-50288000	Strong transcription	Brain Hippocampus Middle	brain
4	chr12:50279200-50288000	Strong transcription	Brain Cingulate Gyrus	brain
5	chr12:50281200-50288000	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr12:50282400-50287800	Weak transcription	A549	lung
7	chr12:50282600-50288200	Strong transcription	Brain Substantia Nigra	brain
8	chr12:50283000-50288000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr12:50283400-50287800	Weak transcription	Esophagus	oesophagus
10	chr12:50283400-50288000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:50283600-50290600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr12:50284000-50288000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr12:50284400-50288400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr12:50285400-50289800	Weak transcription	Fetal Brain Female	brain
15	chr12:50286200-50287800	Weak transcription	Stomach Mucosa	stomach
16	chr12:50286400-50287800	Weak transcription	Spleen	Spleen
17	chr12:50286400-50288000	Strong transcription	Brain Anterior Caudate	brain
18	chr12:50286600-50287600	Weak transcription	Fetal Stomach	stomach
19	chr12:50286600-50288000	Strong transcription	Brain Inferior Temporal Lobe	brain
20	chr12:50286600-50288000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr12:50286600-50288400	Weak transcription	Brain Angular Gyrus	brain
22	chr12:50287000-50292000	Weak transcription	K562	blood
23	chr12:50287000-50295000	Strong transcription	Brain Germinal Matrix	brain
24	chr12:50287200-50287600	Enhancers	Hela-S3	cervix

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