Variant report

Variant	rs2659540
Chromosome Location	chr4:102119690-102119691
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	chr4:102119620-102119792	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:102112038..102115219-chr4:102118263..102121528,3	MCF-7	breast:
2	chr4:102119014..102119905-chr4:102132461..102133442,2	MCF-7	breast:
3	chr4:102115439..102118195-chr4:102118309..102119810,2	MCF-7	breast:

Variant related genes	Relation type
PPP3CA	TF binding region
ENSG00000138814	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1021965	0.85[ASN][1000 genomes]
rs1354785	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1395475	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1395476	0.85[ASN][1000 genomes]
rs1506799	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1506800	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1506802	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1506803	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1506804	0.85[ASN][1000 genomes]
rs1543856	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17030851	0.81[ASN][1000 genomes]
rs2135610	0.85[ASN][1000 genomes]
rs2135614	0.80[ASN][1000 genomes]
rs2174683	0.80[ASN][1000 genomes]
rs2659503	0.85[ASN][1000 genomes]
rs2659504	0.85[ASN][1000 genomes]
rs2659505	0.85[ASN][1000 genomes]
rs2659506	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2659508	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2659509	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2659511	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2659512	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2659513	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2659532	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2659533	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2659534	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2659537	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2659538	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2659539	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2659541	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2659542	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2850980	0.85[ASN][1000 genomes]
rs2850981	0.85[ASN][1000 genomes]
rs2850982	0.85[ASN][1000 genomes]
rs2850985	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2850987	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2850989	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2850990	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2850991	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2850994	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2850995	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3804366	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4478191	0.82[ASN][1000 genomes]
rs73833252	0.83[ASN][1000 genomes]
rs931871	0.80[ASN][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	nsv931418	chr4:101500167-102443207	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv999741	chr4:102009017-102454115	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537199	chr4:102009017-102454115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1004766	chr4:102009017-102713765	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537200	chr4:102009017-102713765	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1011351	chr4:102056024-102450302	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102105400-102126200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr4:102106200-102121600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr4:102107600-102126600	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr4:102109200-102126200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr4:102109800-102122600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr4:102111200-102122400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr4:102113200-102119800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr4:102113200-102119800	Weak transcription	Fetal Brain Male	brain
9	chr4:102113200-102121000	Weak transcription	HSMM	muscle
10	chr4:102113200-102122400	Weak transcription	Aorta	Aorta
11	chr4:102113200-102124400	Weak transcription	Pancreas	Pancrea
12	chr4:102113400-102120400	Weak transcription	Fetal Heart	heart
13	chr4:102113400-102120800	Weak transcription	NH-A	brain
14	chr4:102113600-102120600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr4:102113600-102120800	Weak transcription	Right Ventricle	heart
16	chr4:102113600-102121400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr4:102113600-102122800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr4:102113800-102119800	Weak transcription	Fetal Kidney	kidney
19	chr4:102113800-102120400	Weak transcription	Brain Substantia Nigra	brain
20	chr4:102113800-102120600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr4:102113800-102120800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr4:102113800-102121000	Weak transcription	Stomach Smooth Muscle	stomach
23	chr4:102113800-102121000	Weak transcription	HMEC	breast
24	chr4:102113800-102122800	Weak transcription	Right Atrium	heart
25	chr4:102113800-102126200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr4:102113800-102127200	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr4:102113800-102131800	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr4:102114000-102119800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr4:102114000-102120000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr4:102114000-102120600	Weak transcription	NHDF-Ad	bronchial
31	chr4:102114000-102121200	Weak transcription	Adipose Nuclei	Adipose
32	chr4:102114800-102121200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr4:102115400-102120800	Weak transcription	Osteobl	bone
34	chr4:102117000-102120800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr4:102117000-102121600	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr4:102117200-102119800	Enhancers	A549	lung
37	chr4:102117200-102120200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr4:102117200-102120400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr4:102117200-102120600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr4:102117200-102120600	Weak transcription	NHLF	lung
41	chr4:102117200-102121200	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr4:102117200-102121200	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr4:102117200-102125800	Weak transcription	Dnd41	blood
44	chr4:102117200-102126200	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr4:102117400-102121200	Weak transcription	NHEK	skin
46	chr4:102117600-102121400	Enhancers	Fetal Intestine Small	intestine
47	chr4:102117600-102123000	Enhancers	HepG2	liver
48	chr4:102117800-102121800	Enhancers	Liver	Liver
49	chr4:102117800-102124200	Enhancers	Pancreatic Islets	Pancreatic Islet
50	chr4:102118000-102132600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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