Variant report

Variant	rs3742996
Chromosome Location	chr15:42740369-42740370
allele	A/G
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	POLR2A	chr15:42740242-42740479	K562	blood:	n/a	n/a

Variant related genes	Relation type
ZNF106	TF binding region

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs12101559	0.87[MEX][hapmap];0.85[AMR][1000 genomes]
rs12438240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12438369	0.81[ASW][hapmap]
rs12438509	0.81[ASW][hapmap];0.85[CHB][hapmap]
rs16973008	0.81[ASW][hapmap];0.85[CHB][hapmap]
rs16973045	0.85[CHB][hapmap]
rs16973060	0.85[CHB][hapmap]
rs16973261	0.83[AMR][1000 genomes]
rs2412688	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes]
rs2412709	1.00[ASW][hapmap];1.00[CHD][hapmap];0.86[YRI][hapmap]
rs2617238	1.00[CEU][hapmap]
rs28364393	0.89[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs28745877	1.00[EUR][1000 genomes]
rs3743005	0.81[ASW][hapmap];0.85[CHB][hapmap]
rs3743007	0.85[CHB][hapmap]
rs3743008	0.85[CHB][hapmap]
rs3825785	0.81[ASW][hapmap];0.85[CHB][hapmap]
rs4506867	0.85[CHB][hapmap];0.81[YRI][hapmap]
rs4923945	0.82[CHB][hapmap]
rs4923947	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs4924672	0.81[ASW][hapmap];0.85[CHB][hapmap]
rs4924673	0.85[CHB][hapmap]
rs4924675	0.81[ASW][hapmap];0.81[CHD][hapmap]
rs4924677	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924679	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4924680	0.93[AMR][1000 genomes]
rs4924682	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55671734	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57734638	0.96[AMR][1000 genomes]
rs58567518	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59091866	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59206762	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59414917	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59908459	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60328984	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60634548	0.83[EUR][1000 genomes]
rs61069354	0.83[EUR][1000 genomes]
rs7169767	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7171201	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7180279	0.81[ASW][hapmap];0.85[CHB][hapmap]
rs7180315	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7181688	0.83[AMR][1000 genomes]
rs73402745	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73403365	0.83[EUR][1000 genomes]
rs8026817	0.95[AMR][1000 genomes]
rs8036255	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs934876	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][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	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv832986	chr15:42587825-42753664	Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv832987	chr15:42627447-42792348	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	esv3334708	chr15:42664344-42827738	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42694600-42750600	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr15:42699200-42741600	Strong transcription	Fetal Muscle Trunk	muscle
3	chr15:42700800-42747200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr15:42701200-42766600	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr15:42701600-42744200	Strong transcription	Stomach Smooth Muscle	stomach
6	chr15:42702200-42750200	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr15:42702400-42744200	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr15:42702400-42744200	Strong transcription	Liver	Liver
9	chr15:42702600-42744400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr15:42702800-42744400	Strong transcription	Duodenum Mucosa	Duodenum
11	chr15:42704000-42744400	Strong transcription	Fetal Lung	lung
12	chr15:42704000-42746800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:42704600-42744200	Strong transcription	Primary T helper cells PMA-I stimulated	--
14	chr15:42705800-42749200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr15:42706400-42744200	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr15:42709800-42747000	Weak transcription	Stomach Mucosa	stomach
17	chr15:42711800-42749200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr15:42720400-42759200	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr15:42721000-42744400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr15:42721800-42747400	Strong transcription	HSMM	muscle
21	chr15:42723200-42742000	Weak transcription	Small Intestine	intestine
22	chr15:42724400-42744200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr15:42727400-42745600	Strong transcription	GM12878-XiMat	blood
24	chr15:42729200-42740400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr15:42730800-42746800	Strong transcription	Hela-S3	cervix
26	chr15:42732400-42746200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr15:42732600-42746200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr15:42732800-42744200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr15:42733000-42741000	Strong transcription	Fetal Intestine Small	intestine
30	chr15:42733000-42745200	Strong transcription	Fetal Stomach	stomach
31	chr15:42733200-42741000	Strong transcription	Fetal Intestine Large	intestine
32	chr15:42733200-42744200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr15:42733200-42744200	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr15:42733200-42744200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr15:42733200-42744600	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr15:42733200-42747400	Strong transcription	Placenta	Placenta
37	chr15:42733400-42741400	Strong transcription	Adipose Nuclei	Adipose
38	chr15:42733400-42744200	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr15:42733400-42744400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr15:42733400-42744400	Strong transcription	Fetal Thymus	thymus
41	chr15:42733400-42744400	Strong transcription	NHDF-Ad	bronchial
42	chr15:42733400-42747000	Strong transcription	Primary B cells from peripheral blood	blood
43	chr15:42733400-42747200	Strong transcription	Primary B cells from cord blood	blood
44	chr15:42733400-42748000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr15:42733600-42744200	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr15:42733600-42744200	Strong transcription	Brain Inferior Temporal Lobe	brain
47	chr15:42733600-42744200	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr15:42733600-42744800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr15:42733800-42740800	Strong transcription	Rectal Smooth Muscle	rectum
50	chr15:42734000-42744200	Strong transcription	Thymus	Thymus

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