Variant report

Variant	rs4699116
Chromosome Location	chr4:102108693-102108694
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10005338	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10018021	0.87[EUR][1000 genomes]
rs10025780	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10030389	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs10050301	0.95[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10516471	0.90[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13103902	0.86[EUR][1000 genomes]
rs13111186	0.86[EUR][1000 genomes]
rs13112866	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13118966	0.87[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13125501	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13128841	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs13135924	0.86[EUR][1000 genomes]
rs13142024	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs2048072	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2135611	0.89[JPT][hapmap];0.81[AMR][1000 genomes]
rs2174680	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3804361	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3804368	0.95[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3811063	0.95[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3827770	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4590038	0.86[EUR][1000 genomes]
rs4698912	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs4698913	0.86[EUR][1000 genomes]
rs4699106	0.86[EUR][1000 genomes]
rs4699127	0.95[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7677550	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs950177	0.86[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9884638	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9995338	0.87[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	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:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102079400-102113800	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr4:102090800-102112200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:102090800-102114400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr4:102096200-102112600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:102096600-102112000	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr4:102096600-102112000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr4:102096600-102112000	Weak transcription	Right Ventricle	heart
8	chr4:102097400-102112200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr4:102097800-102112200	Weak transcription	Adipose Nuclei	Adipose
10	chr4:102097800-102112200	Weak transcription	Left Ventricle	heart
11	chr4:102097800-102112600	Weak transcription	Pancreas	Pancrea
12	chr4:102098600-102109800	Weak transcription	HepG2	liver
13	chr4:102098600-102118600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr4:102102000-102109800	Weak transcription	Esophagus	oesophagus
15	chr4:102102000-102112200	Weak transcription	Psoas Muscle	Psoas
16	chr4:102102000-102112800	Weak transcription	Right Atrium	heart
17	chr4:102102200-102110600	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr4:102102200-102112200	Weak transcription	Aorta	Aorta
19	chr4:102102200-102116400	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr4:102104000-102112200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr4:102104200-102112200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr4:102104200-102112800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr4:102104200-102116200	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr4:102104400-102112600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr4:102104400-102119400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr4:102104400-102119600	Weak transcription	Primary T cells from cord blood	blood
27	chr4:102104400-102119600	Weak transcription	Ovary	ovary
28	chr4:102104600-102112200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr4:102104600-102112400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr4:102104600-102114000	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr4:102104600-102116400	Weak transcription	Dnd41	blood
32	chr4:102104800-102109000	Enhancers	A549	lung
33	chr4:102105400-102109000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr4:102105400-102112200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr4:102105400-102113000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr4:102105400-102117800	Weak transcription	Primary hematopoietic stem cells	blood
37	chr4:102105400-102126200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr4:102105600-102109000	Weak transcription	Colon Smooth Muscle	Colon
39	chr4:102105600-102112600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr4:102105600-102112800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr4:102106200-102109000	Weak transcription	NHEK	skin
42	chr4:102106200-102111000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr4:102106200-102111400	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr4:102106200-102112400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr4:102106200-102112800	Weak transcription	Duodenum Mucosa	Duodenum
46	chr4:102106200-102113000	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr4:102106200-102113000	Weak transcription	HMEC	breast
48	chr4:102106200-102117600	Weak transcription	Gastric	stomach
49	chr4:102106200-102121600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr4:102106600-102112200	Weak transcription	HUES48 Cell Line	embryonic stem cell

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