Variant report

Variant	rs2433415
Chromosome Location	chr11:86410905-86410906
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr11:86410389-86411040	MCF-7	breast:	n/a	n/a
2	HDAC2	chr11:86410263-86410938	MCF-7	breast:	n/a	n/a
3	SRF	chr11:86410318-86410963	MCF-7	breast:	n/a	chr11:86410805-86410823 chr11:86410595-86410608 chr11:86410596-86410613 chr11:86410597-86410611
4	FOXA1	chr11:86410314-86410911	T-47D	breast:	n/a	chr11:86410632-86410647
5	GATA3	chr11:86410404-86410924	MCF-7	breast:	n/a	n/a
6	SIN3AK20	chr11:86410181-86411063	MCF-7	breast:	n/a	n/a
7	EP300	chr11:86410375-86410918	T-47D	breast:	n/a	n/a
8	NR2F2	chr11:86410265-86410928	MCF-7	breast:	n/a	n/a
9	GATA3	chr11:86410218-86411023	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:86410588..86412313-chr11:86452715..86455271,2	K562	blood:
2	chr11:86407227..86410961-chr11:86511491..86515054,3	MCF-7	breast:
3	chr11:86410023..86412517-chr11:86415107..86418270,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254731	TF binding region
ENSG00000150687	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10501626	0.93[CHB][hapmap]
rs10898526	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11234738	0.95[ASN][1000 genomes]
rs11234739	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11234741	0.98[ASN][1000 genomes]
rs11234743	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11234744	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs11234745	0.89[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11234746	0.98[ASN][1000 genomes]
rs12574672	0.93[ASN][1000 genomes]
rs12575285	0.93[CHB][hapmap]
rs12789412	0.95[ASN][1000 genomes]
rs17211458	0.93[CHB][hapmap]
rs17818845	0.87[CHB][hapmap]
rs17819523	0.93[CHB][hapmap]
rs17819683	0.93[CHB][hapmap]
rs1945142	0.93[CHB][hapmap]
rs2433412	0.99[ASN][1000 genomes]
rs2433413	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2433414	1.00[ASN][1000 genomes]
rs4619178	0.99[ASN][1000 genomes]
rs539214	0.87[CHB][hapmap]
rs543336	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs544199	0.94[ASN][1000 genomes]
rs575273	0.94[ASN][1000 genomes]
rs575468	0.94[ASN][1000 genomes]
rs600242	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs602498	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs659301	0.87[CHB][hapmap]
rs66878934	0.88[ASN][1000 genomes]
rs672266	0.87[CHB][hapmap]
rs67655324	0.91[ASN][1000 genomes]
rs72961766	0.85[ASN][1000 genomes]
rs72961771	0.93[ASN][1000 genomes]
rs746491	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7933920	0.96[ASN][1000 genomes]
rs7939319	0.98[ASN][1000 genomes]
rs7948924	0.95[ASN][1000 genomes]
rs949348	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044081	chr11:86133641-86868560	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv541118	chr11:86133641-86868560	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv555665	chr11:86230898-86417553	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1055071	chr11:86301240-86465465	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv428263	chr11:86357990-86508480	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1049157	chr11:86409059-86504155	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	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
rs2433415	CCDC83	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86385200-86411400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr11:86386600-86431000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr11:86399600-86415800	Weak transcription	Fetal Heart	heart
4	chr11:86400600-86414800	Weak transcription	Ovary	ovary
5	chr11:86405600-86411200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr11:86407000-86451600	Weak transcription	Left Ventricle	heart
7	chr11:86407600-86412800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr11:86407600-86417000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr11:86408000-86413200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr11:86408000-86431400	Weak transcription	Aorta	Aorta
11	chr11:86408200-86413200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr11:86408400-86412400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr11:86408400-86413200	Weak transcription	NHLF	lung
14	chr11:86408600-86412600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr11:86409600-86411000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr11:86409600-86411000	Enhancers	HMEC	breast
17	chr11:86409600-86413000	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr11:86409800-86411000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr11:86410200-86411000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr11:86410200-86411200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr11:86410200-86413200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr11:86410600-86412600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr11:86410600-86412600	Weak transcription	NHDF-Ad	bronchial
24	chr11:86410600-86413000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr11:86410600-86419800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr11:86410800-86411000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr11:86410800-86411200	Enhancers	Psoas Muscle	Psoas
28	chr11:86410800-86411600	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr11:86410800-86411600	Enhancers	Colon Smooth Muscle	Colon
30	chr11:86410800-86412600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr11:86410800-86416400	Weak transcription	A549	lung
32	chr11:86410800-86419400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr11:86410800-86420200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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