Variant report

Variant	rs10006159
Chromosome Location	chr4:16231139-16231140
allele	C/T
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	chr4:16231131-16231494	GM12878	blood:	n/a	n/a
2	POLR2A	chr4:16228635-16234024	K562	blood:	n/a	n/a
3	POLR2A	chr4:16230349-16232360	MCF10A-Er-Src	breast:	n/a	n/a
4	IRF1	chr4:16231118-16231285	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:16230982..16233844-chr4:16235259..16238422,3	MCF-7	breast:
2	chr4:16230488..16232179-chr4:16234227..16236390,2	MCF-7	breast:
3	chr4:16227416..16229454-chr4:16230827..16235422,5	MCF-7	breast:

Variant related genes	Relation type
TAPT1	TF binding region
ENSG00000263327	Chromatin interaction
ENSG00000169762	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10019399	0.82[YRI][hapmap]
rs1025897	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10939657	0.89[ASN][1000 genomes]
rs11730977	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13133263	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13634	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[EUR][1000 genomes]
rs1618243	0.83[EUR][1000 genomes]
rs1662654	0.80[YRI][hapmap]
rs16893162	0.85[YRI][hapmap]
rs1712492	0.91[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs178450	0.80[YRI][hapmap]
rs203434	0.91[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.80[YRI][hapmap];0.95[AFR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs203435	0.86[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs317853	0.84[EUR][1000 genomes]
rs317854	0.82[YRI][hapmap]
rs317869	0.80[YRI][hapmap]
rs317870	0.82[YRI][hapmap]
rs317872	0.82[YRI][hapmap]
rs317873	0.91[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs317875	0.82[YRI][hapmap]
rs317876	0.82[YRI][hapmap]
rs317877	0.81[YRI][hapmap]
rs36012247	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4317201	0.84[ASN][1000 genomes]
rs6812660	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7666361	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs961449	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004821	chr4:16055996-16830629	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv537046	chr4:16055996-16830629	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv537047	chr4:16182060-16375787	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv878720	chr4:16222046-16242215	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv537048	chr4:16226406-16375787	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv593778	chr4:16227851-16233787	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv967728	chr4:16229943-16232845	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:16229400-16231600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:16229400-16241000	Weak transcription	Aorta	Aorta
3	chr4:16229600-16233000	Weak transcription	Colon Smooth Muscle	Colon
4	chr4:16229600-16233200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr4:16229600-16233400	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr4:16229600-16233400	Weak transcription	Right Atrium	heart
7	chr4:16229600-16234200	Weak transcription	Brain Germinal Matrix	brain
8	chr4:16229600-16235400	Weak transcription	Left Ventricle	heart
9	chr4:16229600-16237600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr4:16229600-16254000	Weak transcription	Ovary	ovary
11	chr4:16229600-16254800	Weak transcription	Psoas Muscle	Psoas
12	chr4:16229800-16233000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr4:16229800-16233000	Weak transcription	HUVEC	blood vessel
14	chr4:16229800-16233000	Weak transcription	NHDF-Ad	bronchial
15	chr4:16229800-16233200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr4:16229800-16233200	Weak transcription	Osteobl	bone
17	chr4:16229800-16233400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr4:16229800-16233800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:16229800-16233800	Weak transcription	Fetal Kidney	kidney
20	chr4:16229800-16241400	Weak transcription	Primary T cells from cord blood	blood
21	chr4:16229800-16259800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr4:16230000-16231200	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr4:16230000-16231200	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr4:16230000-16232000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr4:16230000-16232000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr4:16230000-16232800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr4:16230000-16233000	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr4:16230000-16233200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr4:16230000-16233200	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr4:16230000-16233200	Weak transcription	Stomach Mucosa	stomach
31	chr4:16230000-16233400	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr4:16230000-16233800	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr4:16230000-16237000	Weak transcription	Fetal Brain Female	brain
34	chr4:16230000-16238000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr4:16230000-16244200	Weak transcription	Pancreas	Pancrea
36	chr4:16230000-16244800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr4:16230000-16244800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr4:16230200-16232600	Weak transcription	Fetal Brain Male	brain
39	chr4:16230200-16233000	Weak transcription	Adipose Nuclei	Adipose
40	chr4:16230200-16233200	Enhancers	Brain Hippocampus Middle	brain
41	chr4:16230200-16233600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr4:16230200-16233800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr4:16230600-16231400	Weak transcription	Brain Cingulate Gyrus	brain
44	chr4:16230600-16231600	Weak transcription	Primary B cells from peripheral blood	blood
45	chr4:16230600-16231600	Weak transcription	Liver	Liver
46	chr4:16230600-16232800	Weak transcription	Brain Substantia Nigra	brain
47	chr4:16230600-16233200	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr4:16230600-16233400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr4:16230600-16233600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr4:16230600-16233800	Weak transcription	Duodenum Mucosa	Duodenum

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