Variant report

Variant	rs10485442
Chromosome Location	chr20:52564250-52564251
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:52562683..52565163-chr6:10527281..10529505,2	MCF-7	breast:
2	chr20:52562034..52564682-chr20:55844652..55847226,2	MCF-7	breast:
3	chr20:52551745..52571491-chr20:55837843..55848700,39	MCF-7	breast:
4	chr20:52555643..52557522-chr20:52563500..52566122,2	K562	blood:
5	chr20:52563468..52566159-chr20:52815919..52818201,3	MCF-7	breast:
6	chr20:52563890..52565885-chr20:52722350..52724626,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101144	Chromatin interaction
ENSG00000111846	Chromatin interaction
ENSG00000236352	Chromatin interaction
ENSG00000226308	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12480336	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2072241	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2276516	0.87[CEU][hapmap];0.89[MEX][hapmap]
rs6123330	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases
2	nsv834009	chr20:52386050-52590795	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	182 gene(s)	inside rSNPs	diseases
3	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
4	nsv1055549	chr20:52555871-52586281	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10485442	BCAS1	cis	parietal	SCAN
rs10485442	CSTF1	cis	cerebellum	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52552000-52565200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr20:52552200-52565400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr20:52552400-52566000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr20:52552600-52564400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr20:52554800-52565000	Weak transcription	Spleen	Spleen
6	chr20:52556400-52565400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr20:52556600-52566000	Weak transcription	Aorta	Aorta
8	chr20:52557200-52565000	Weak transcription	Left Ventricle	heart
9	chr20:52557400-52569200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr20:52557800-52565400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr20:52558000-52565000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr20:52558000-52565400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr20:52558000-52565400	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr20:52558000-52565800	Weak transcription	Colonic Mucosa	Colon
15	chr20:52558000-52566000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr20:52558400-52569000	Weak transcription	Fetal Intestine Small	intestine
17	chr20:52558800-52565200	Weak transcription	Small Intestine	intestine
18	chr20:52559000-52565400	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr20:52559200-52565400	Weak transcription	Right Atrium	heart
20	chr20:52559400-52565000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr20:52559400-52565000	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr20:52560000-52565200	Weak transcription	NHDF-Ad	bronchial
23	chr20:52560000-52565400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr20:52560000-52566200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr20:52560400-52565000	Weak transcription	HMEC	breast
26	chr20:52560600-52565200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr20:52560800-52564400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr20:52560800-52564400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr20:52560800-52564400	Weak transcription	GM12878-XiMat	blood
30	chr20:52560800-52564600	Weak transcription	Primary hematopoietic stem cells	blood
31	chr20:52560800-52564600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr20:52560800-52564600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr20:52560800-52565200	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr20:52560800-52565200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr20:52560800-52565200	Weak transcription	Duodenum Mucosa	Duodenum
36	chr20:52560800-52565200	Weak transcription	HSMM	muscle
37	chr20:52560800-52565200	Weak transcription	HUVEC	blood vessel
38	chr20:52560800-52565200	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr20:52560800-52565200	Weak transcription	NH-A	brain
40	chr20:52560800-52565200	Weak transcription	NHEK	skin
41	chr20:52560800-52565200	Weak transcription	Osteobl	bone
42	chr20:52560800-52565400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr20:52560800-52565400	Weak transcription	Primary B cells from cord blood	blood
44	chr20:52560800-52565400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr20:52560800-52565400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr20:52560800-52565400	Weak transcription	NHLF	lung
47	chr20:52560800-52565600	Weak transcription	Brain Angular Gyrus	brain
48	chr20:52560800-52565600	Weak transcription	Brain Substantia Nigra	brain
49	chr20:52561000-52564600	Weak transcription	Fetal Stomach	stomach
50	chr20:52561000-52564600	Weak transcription	Stomach Mucosa	stomach

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