Variant report

Variant	rs4241545
Chromosome Location	chr3:20107205-20107206
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:20105530..20108149-chr3:20143893..20147714,3	MCF-7	breast:
2	chr3:20080894..20083209-chr3:20107151..20110064,3	K562	blood:
3	chr3:20102932..20104698-chr3:20105187..20107405,2	K562	blood:

Variant related genes	Relation type
ENSG00000114166	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11713069	1.00[ASN][1000 genomes]
rs12486167	1.00[LWK][hapmap]
rs13066876	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13066923	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13069629	1.00[ASN][1000 genomes]
rs13095743	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13096876	1.00[ASN][1000 genomes]
rs13097157	1.00[ASN][1000 genomes]
rs13097409	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[ASN][1000 genomes]
rs13098588	1.00[ASN][1000 genomes]
rs17180771	1.00[LWK][hapmap]
rs17182383	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17627750	0.83[ASN][1000 genomes]
rs17627906	0.83[ASN][1000 genomes]
rs17627936	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs17678713	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];0.83[ASN][1000 genomes]
rs17796230	1.00[LWK][hapmap]
rs17796904	1.00[ASN][1000 genomes]
rs17804451	1.00[ASN][1000 genomes]
rs34204839	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34515517	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34572705	1.00[ASN][1000 genomes]
rs35424474	1.00[ASN][1000 genomes]
rs35632245	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35645247	1.00[ASN][1000 genomes]
rs35659955	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35776229	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35841175	1.00[ASN][1000 genomes]
rs36029475	1.00[ASN][1000 genomes]
rs3849533	1.00[LWK][hapmap]
rs3960789	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41285061	1.00[ASN][1000 genomes]
rs4858156	1.00[ASN][1000 genomes]
rs4858751	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858752	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858755	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858763	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4858765	1.00[ASN][1000 genomes]
rs4858768	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[ASN][1000 genomes]
rs55812129	0.83[ASN][1000 genomes]
rs71316246	1.00[ASN][1000 genomes]
rs71316248	1.00[ASN][1000 genomes]
rs71316249	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1825914	chr3:19549859-20137270	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	esv1833139	chr3:19579860-20121349	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	esv1826030	chr3:19972766-20170581	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	esv1826830	chr3:19982972-20632072	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv997486	chr3:20006702-20113989	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	esv1829542	chr3:20009231-20384627	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
9	nsv834627	chr3:20068115-20227975	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	nsv433359	chr3:20090908-20587572	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
11	nsv470450	chr3:20096735-20389045	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer 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	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4241545	C3orf48	cis	cerebellum	SCAN
rs4241545	UBE2E2	cis	parietal	SCAN
rs4241545	KAT2B	cis	parietal	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:20099000-20122600	Weak transcription	Aorta	Aorta
2	chr3:20099400-20108600	Weak transcription	Fetal Stomach	stomach
3	chr3:20099400-20112600	Weak transcription	HSMMtube	muscle
4	chr3:20099400-20112800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:20099400-20122600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr3:20099400-20122800	Weak transcription	Lung	lung
7	chr3:20100000-20109200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr3:20102800-20113400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr3:20102800-20136800	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr3:20103000-20108400	Weak transcription	Fetal Thymus	thymus
11	chr3:20103000-20108400	Weak transcription	Osteobl	bone
12	chr3:20103000-20111400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr3:20103200-20107600	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr3:20103200-20108400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:20103200-20108400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:20103200-20108600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:20103200-20108600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:20103200-20108600	Weak transcription	NHDF-Ad	bronchial
19	chr3:20103200-20108800	Weak transcription	A549	lung
20	chr3:20103200-20110400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr3:20103200-20112600	Weak transcription	Primary T cells from cord blood	blood
22	chr3:20103200-20112800	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr3:20103200-20113000	Weak transcription	Primary B cells from cord blood	blood
24	chr3:20103200-20113000	Weak transcription	Primary hematopoietic stem cells	blood
25	chr3:20103200-20113000	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr3:20103200-20113200	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr3:20103200-20114000	Weak transcription	Liver	Liver
28	chr3:20103200-20119400	Weak transcription	Fetal Intestine Small	intestine
29	chr3:20103200-20122200	Weak transcription	Duodenum Mucosa	Duodenum
30	chr3:20104000-20111000	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr3:20104200-20107800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr3:20104200-20111800	Enhancers	Brain Substantia Nigra	brain
33	chr3:20104400-20108200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:20104400-20113400	Enhancers	Brain Hippocampus Middle	brain
35	chr3:20105000-20111000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:20105200-20110800	Enhancers	HMEC	breast
37	chr3:20105400-20108000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr3:20105400-20108000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr3:20105800-20108200	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr3:20105800-20108400	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr3:20105800-20113200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr3:20106000-20108000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr3:20106000-20108600	Enhancers	Fetal Muscle Leg	muscle
44	chr3:20106000-20109200	Enhancers	Brain Anterior Caudate	brain
45	chr3:20106000-20111400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr3:20106400-20107400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr3:20106400-20107400	Enhancers	Colon Smooth Muscle	Colon
48	chr3:20106400-20107800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr3:20106400-20108200	Enhancers	Ovary	ovary
50	chr3:20106400-20108200	Enhancers	Psoas Muscle	Psoas

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