Variant report

Variant	rs2929403
Chromosome Location	chr3:20095914-20095915
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:20094893..20096727-chr3:20227964..20230863,2	MCF-7	breast:
2	chr3:20087468..20090751-chr3:20095333..20097422,3	MCF-7	breast:
3	chr3:19987759..19990074-chr3:20094320..20096186,3	MCF-7	breast:
4	chr3:19919756..19921311-chr3:20094992..20097825,2	K562	blood:

Variant related genes	Relation type
ENSG00000163576	Chromatin interaction
ENSG00000144566	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11128936	0.90[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11714203	0.87[ASN][1000 genomes]
rs1610186	0.88[JPT][hapmap]
rs2293139	0.90[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2365793	0.82[AMR][1000 genomes]
rs2623075	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2661376	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2661377	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs2686315	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2929399	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2929400	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2929405	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2948083	0.98[EUR][1000 genomes]
rs2948086	0.95[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs2948087	0.90[CEU][hapmap];0.98[EUR][1000 genomes]
rs2948088	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59213344	0.86[ASN][1000 genomes]
rs60355368	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784715	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs939851	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs977162	1.00[JPT][hapmap]
rs9829896	1.00[JPT][hapmap]

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	esv1825988	chr3:19976375-20102773	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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
11	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

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:20083000-20098600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:20085200-20098200	Weak transcription	Fetal Kidney	kidney
3	chr3:20085400-20096000	Weak transcription	Pancreas	Pancrea
4	chr3:20085800-20096000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr3:20086200-20096000	Weak transcription	Lung	lung
6	chr3:20086200-20096800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:20086200-20102800	Weak transcription	Fetal Intestine Small	intestine
8	chr3:20086400-20096000	Weak transcription	K562	blood
9	chr3:20087600-20099400	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr3:20088200-20096000	Weak transcription	Primary T cells from cord blood	blood
11	chr3:20089800-20096000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr3:20089800-20096200	Weak transcription	Brain Germinal Matrix	brain
13	chr3:20090200-20096000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr3:20090200-20096400	Weak transcription	Fetal Brain Male	brain
15	chr3:20090200-20096400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr3:20090200-20098400	Weak transcription	Ovary	ovary
17	chr3:20090400-20096400	Weak transcription	Fetal Stomach	stomach
18	chr3:20090600-20096000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr3:20090800-20096000	Weak transcription	Small Intestine	intestine
20	chr3:20090800-20099200	Weak transcription	Fetal Muscle Trunk	muscle
21	chr3:20090800-20100600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr3:20091200-20096000	Weak transcription	GM12878-XiMat	blood
23	chr3:20092000-20096000	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr3:20092200-20096200	Weak transcription	Colon Smooth Muscle	Colon
25	chr3:20092600-20096000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr3:20093000-20096400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr3:20093200-20096000	Weak transcription	Esophagus	oesophagus
28	chr3:20093200-20096000	Weak transcription	Gastric	stomach
29	chr3:20093200-20096000	Weak transcription	Right Atrium	heart
30	chr3:20093200-20096000	Weak transcription	Right Ventricle	heart
31	chr3:20094000-20097600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr3:20094200-20099400	Enhancers	Fetal Thymus	thymus
33	chr3:20094400-20096000	Weak transcription	Colonic Mucosa	Colon
34	chr3:20094600-20096000	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr3:20095200-20098400	Enhancers	Muscle Satellite Cultured Cells	--
36	chr3:20095400-20096000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr3:20095400-20096200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr3:20095400-20096400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr3:20095400-20096400	Enhancers	Brain Anterior Caudate	brain
40	chr3:20095400-20099600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr3:20095600-20096000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr3:20095600-20096200	Enhancers	Thymus	Thymus
43	chr3:20095600-20097200	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr3:20095600-20097200	Enhancers	Left Ventricle	heart
45	chr3:20095600-20097200	Enhancers	Monocytes-CD14+_RO01746	blood
46	chr3:20095600-20097600	Enhancers	Primary B cells from cord blood	blood
47	chr3:20095600-20099000	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr3:20095600-20099400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr3:20095600-20099600	Enhancers	Liver	Liver
50	chr3:20095600-20099800	Enhancers	Primary T helper naive cells from peripheral blood	blood

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