Variant report

Variant	rs4695402
Chromosome Location	chr4:48779942-48779943
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:48590381..48593753-chr4:48779651..48782070,3	K562	blood:
2	chr4:48683162..48685673-chr4:48779626..48783041,3	MCF-7	breast:
3	chr4:48774500..48780275-chr4:48780685..48784374,5	MCF-7	breast:
4	chr4:48590381..48593242-chr4:48779651..48782070,2	K562	blood:
5	chr4:48779823..48782624-chr4:48905090..48909886,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145247	Chromatin interaction
ENSG00000075539	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10029425	1.00[AMR][1000 genomes]
rs10034207	1.00[AMR][1000 genomes]
rs10049760	1.00[AMR][1000 genomes]
rs10805171	1.00[AMR][1000 genomes]
rs10805172	1.00[AMR][1000 genomes]
rs10938535	1.00[AMR][1000 genomes]
rs10938538	1.00[AMR][1000 genomes]
rs10938539	1.00[AMR][1000 genomes]
rs10938541	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12500224	1.00[AMR][1000 genomes]
rs12500244	1.00[AMR][1000 genomes]
rs12507475	1.00[AMR][1000 genomes]
rs12507546	1.00[AMR][1000 genomes]
rs1474072	1.00[AMR][1000 genomes]
rs1517673	1.00[AMR][1000 genomes]
rs1517676	1.00[AMR][1000 genomes]
rs1517677	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1533511	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1554257	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1616561	1.00[AMR][1000 genomes]
rs1702796	1.00[AMR][1000 genomes]
rs1702799	1.00[AMR][1000 genomes]
rs1712771	1.00[AMR][1000 genomes]
rs1949422	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2138866	1.00[AMR][1000 genomes]
rs2138867	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28371079	1.00[AMR][1000 genomes]
rs2883410	1.00[AMR][1000 genomes]
rs2940319	1.00[AMR][1000 genomes]
rs4235155	1.00[AMR][1000 genomes]
rs4235157	1.00[AMR][1000 genomes]
rs4330326	1.00[AMR][1000 genomes]
rs4558842	1.00[AMR][1000 genomes]
rs4694896	1.00[AMR][1000 genomes]
rs4694898	1.00[AMR][1000 genomes]
rs4694903	1.00[AMR][1000 genomes]
rs4695385	1.00[AMR][1000 genomes]
rs4695386	1.00[AMR][1000 genomes]
rs4695390	1.00[AMR][1000 genomes]
rs4695403	1.00[AMR][1000 genomes]
rs4695405	1.00[AMR][1000 genomes]
rs6447642	1.00[AMR][1000 genomes]
rs6447654	1.00[AMR][1000 genomes]
rs6447656	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6447657	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6823351	1.00[AMR][1000 genomes]
rs6827481	1.00[AMR][1000 genomes]
rs6828500	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6835757	1.00[AMR][1000 genomes]
rs6844088	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6846797	1.00[AMR][1000 genomes]
rs6848222	1.00[AMR][1000 genomes]
rs6848417	1.00[AMR][1000 genomes]
rs6853876	1.00[AMR][1000 genomes]
rs707720	1.00[AMR][1000 genomes]
rs7664507	1.00[AMR][1000 genomes]
rs7689293	1.00[AMR][1000 genomes]
rs7689662	1.00[AMR][1000 genomes]
rs7692480	1.00[AMR][1000 genomes]
rs7698064	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs776581	1.00[AMR][1000 genomes]
rs776583	1.00[AMR][1000 genomes]
rs776587	1.00[AMR][1000 genomes]
rs776589	1.00[AMR][1000 genomes]
rs776595	1.00[AMR][1000 genomes]
rs776603	1.00[AMR][1000 genomes]
rs938791	1.00[AMR][1000 genomes]
rs9994214	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9998178	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002674	chr4:48507608-49032909	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv537087	chr4:48507608-49032909	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1010923	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv537088	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1013762	chr4:48580484-49032909	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv537089	chr4:48580484-49032909	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS 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	16 gene(s)	inside rSNPs	diseases
7	esv1793455	chr4:48686817-48859142	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1010381	chr4:48701525-49309842	Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv1003718	chr4:48771947-49083089	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48768000-48780800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr4:48768600-48780000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:48768600-48780800	Weak transcription	Gastric	stomach
4	chr4:48768800-48780000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr4:48768800-48780000	Weak transcription	Colonic Mucosa	Colon
6	chr4:48769600-48780400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr4:48772800-48780400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr4:48773400-48780400	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr4:48776000-48780800	Weak transcription	Lung	lung
10	chr4:48776200-48780400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr4:48776600-48780000	Enhancers	Liver	Liver
12	chr4:48776600-48780400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr4:48776800-48780400	Enhancers	Fetal Heart	heart
14	chr4:48777000-48780000	Enhancers	HepG2	liver
15	chr4:48777000-48780400	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr4:48777200-48780000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr4:48777200-48780000	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr4:48777200-48780000	Enhancers	Fetal Intestine Small	intestine
19	chr4:48777200-48781000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr4:48777400-48780000	Enhancers	Fetal Thymus	thymus
21	chr4:48777400-48780000	Weak transcription	Stomach Mucosa	stomach
22	chr4:48777400-48780200	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr4:48777600-48780600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:48778200-48780000	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr4:48778200-48780000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr4:48778400-48780000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr4:48778400-48780000	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr4:48778400-48780000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr4:48778400-48780000	Enhancers	NH-A	brain
30	chr4:48778400-48780400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
31	chr4:48778400-48780400	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr4:48778600-48780400	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr4:48778600-48780400	Flanking Active TSS	Dnd41	blood
34	chr4:48778600-48783400	Active TSS	Brain Substantia Nigra	brain
35	chr4:48778800-48780000	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr4:48778800-48780000	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr4:48778800-48781400	Active TSS	Right Atrium	heart
38	chr4:48778800-48783200	Active TSS	GM12878-XiMat	blood
39	chr4:48778800-48783600	Active TSS	Right Ventricle	heart
40	chr4:48779000-48780000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr4:48779000-48780600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr4:48779000-48780800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
43	chr4:48779000-48780800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
44	chr4:48779200-48780000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr4:48779200-48780200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr4:48779200-48780200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
47	chr4:48779200-48780400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr4:48779200-48781200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr4:48779200-48783400	Active TSS	Aorta	Aorta
50	chr4:48779200-48783600	Active TSS	Brain Inferior Temporal Lobe	brain

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