Variant report

Variant	rs2072241
Chromosome Location	chr20:52561372-52561373
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52560794..52562724-chr20:52567019..52569815,2	K562	blood:
2	chr20:52368008..52370445-chr20:52559869..52562207,2	K562	blood:
3	chr20:52561105..52561751-chr20:52678984..52679783,3	MCF-7	breast:
4	chr17:59474996..59480161-chr20:52556121..52561884,6	MCF-7	breast:
5	chr20:52560304..52562724-chr20:52567019..52568776,2	K562	blood:
6	chr20:52551745..52571491-chr20:55837843..55848700,39	MCF-7	breast:
7	chr20:52560480..52562741-chr20:55768804..55771635,2	MCF-7	breast:
8	chr17:59938922..59941556-chr20:52559570..52562678,4	MCF-7	breast:
9	chr20:52559752..52562075-chr20:52740413..52742422,2	MCF-7	breast:
10	chr20:52557746..52563146-chr20:52657006..52659772,4	MCF-7	breast:
11	chr17:65105910..65108534-chr20:52559281..52562207,2	MCF-7	breast:
12	chr20:52558981..52564129-chr20:55836783..55844481,11	MCF-7	breast:
13	chr20:52195029..52195939-chr20:52561371..52562333,2	MCF-7	breast:
14	chr19:36979934..36982567-chr20:52560633..52562262,2	MCF-7	breast:
15	chr20:46426563..46428367-chr20:52559861..52561851,2	MCF-7	breast:
16	chr20:52560012..52562267-chr20:55711106..55712686,2	MCF-7	breast:
17	chr20:52559436..52563204-chr20:52814345..52818014,8	MCF-7	breast:
18	chr20:52560247..52562300-chr20:55803016..55805479,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000267280	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000267309	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000186017	Chromatin interaction
ENSG00000267131	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000136492	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10485442	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]
rs1055253	0.83[ASW][hapmap]
rs12480336	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv820262	chr20:52560768-52561389	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2072241	BCAS1	cis	parietal	SCAN
rs2072241	CSTF1	cis	cerebellum	SCAN

Chromatin state (count:83 , 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	chr20:52556400-52564000	Weak transcription	Esophagus	oesophagus
7	chr20:52556400-52564000	Weak transcription	Gastric	stomach
8	chr20:52556400-52565400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr20:52556600-52566000	Weak transcription	Aorta	Aorta
10	chr20:52556800-52564000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr20:52557000-52564200	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr20:52557200-52565000	Weak transcription	Left Ventricle	heart
13	chr20:52557400-52569200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr20:52557800-52565400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr20:52558000-52565000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr20:52558000-52565400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr20:52558000-52565400	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr20:52558000-52565800	Weak transcription	Colonic Mucosa	Colon
19	chr20:52558000-52566000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr20:52558400-52569000	Weak transcription	Fetal Intestine Small	intestine
21	chr20:52558800-52564200	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr20:52558800-52565200	Weak transcription	Small Intestine	intestine
23	chr20:52559000-52565400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr20:52559200-52565400	Weak transcription	Right Atrium	heart
25	chr20:52559400-52565000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr20:52559400-52565000	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr20:52560000-52564000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr20:52560000-52565200	Weak transcription	NHDF-Ad	bronchial
29	chr20:52560000-52565400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr20:52560000-52566200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr20:52560400-52561600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr20:52560400-52565000	Weak transcription	HMEC	breast
33	chr20:52560600-52565200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr20:52560800-52564000	Weak transcription	Primary T cells from cord blood	blood
35	chr20:52560800-52564000	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr20:52560800-52564000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr20:52560800-52564000	Weak transcription	Brain Hippocampus Middle	brain
38	chr20:52560800-52564200	Weak transcription	HepG2	liver
39	chr20:52560800-52564400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr20:52560800-52564400	Weak transcription	Brain Cingulate Gyrus	brain
41	chr20:52560800-52564400	Weak transcription	GM12878-XiMat	blood
42	chr20:52560800-52564600	Weak transcription	Primary hematopoietic stem cells	blood
43	chr20:52560800-52564600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr20:52560800-52564600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr20:52560800-52565200	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr20:52560800-52565200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr20:52560800-52565200	Weak transcription	Duodenum Mucosa	Duodenum
48	chr20:52560800-52565200	Weak transcription	HSMM	muscle
49	chr20:52560800-52565200	Weak transcription	HUVEC	blood vessel
50	chr20:52560800-52565200	Weak transcription	Monocytes-CD14+_RO01746	blood

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