Variant report

Variant	rs4165
Chromosome Location	chr4:129942088-129942089
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10028124	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10857134	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12650832	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13132428	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1450727	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1699390	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1699396	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1709416	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1709417	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1757941	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs175964	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1947269	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2218814	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2592953	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2592955	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2592956	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs280592	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs280598	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs280600	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs280602	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2893267	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3099898	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3119696	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4975192	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4975287	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4975288	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4975289	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4975290	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4975291	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4975292	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs498435	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62316963	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62318666	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6814109	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6817901	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6820403	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6820637	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6821814	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6830229	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7671455	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7691218	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs789986	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1030513	chr4:129770961-129965026	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv534538	chr4:129799138-130431688	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv522694	chr4:129862073-129994690	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv879931	chr4:129939775-130178102	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129917400-129942400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr4:129932000-129944000	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr4:129932200-129947000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr4:129933200-129942200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr4:129934000-129942400	Weak transcription	Brain Hippocampus Middle	brain
6	chr4:129934200-129942600	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr4:129934200-129944200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr4:129934600-129944200	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr4:129934600-129944200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr4:129935000-129942200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr4:129935600-129943400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr4:129935800-129943800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr4:129935800-129944400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr4:129936000-129943400	Weak transcription	Fetal Heart	heart
15	chr4:129936600-129942200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr4:129936600-129942200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr4:129936600-129942600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr4:129936800-129942200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr4:129936800-129942200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr4:129936800-129942200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr4:129936800-129942200	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr4:129936800-129942200	Weak transcription	Dnd41	blood
23	chr4:129936800-129942800	Weak transcription	Placenta	Placenta
24	chr4:129936800-129943800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr4:129936800-129944000	Weak transcription	NHLF	lung
26	chr4:129937000-129942200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr4:129937000-129942200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr4:129937000-129942200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr4:129937000-129942200	Weak transcription	Esophagus	oesophagus
30	chr4:129937000-129942200	Weak transcription	Pancreas	Pancrea
31	chr4:129937000-129942200	Weak transcription	Thymus	Thymus
32	chr4:129937000-129942200	Weak transcription	Spleen	Spleen
33	chr4:129937000-129942400	Weak transcription	Liver	Liver
34	chr4:129937000-129942600	Weak transcription	Duodenum Mucosa	Duodenum
35	chr4:129937000-129942600	Weak transcription	Left Ventricle	heart
36	chr4:129937000-129942800	Weak transcription	Colonic Mucosa	Colon
37	chr4:129937000-129943000	Weak transcription	Brain Angular Gyrus	brain
38	chr4:129937200-129942200	Weak transcription	Fetal Stomach	stomach
39	chr4:129937200-129942800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr4:129937200-129943200	Weak transcription	Fetal Lung	lung
41	chr4:129937200-129964000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr4:129937800-129942200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr4:129937800-129943800	Weak transcription	Adipose Nuclei	Adipose
44	chr4:129937800-129947000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr4:129939200-129943200	Weak transcription	A549	lung
46	chr4:129939200-129943600	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr4:129939400-129942200	Weak transcription	Aorta	Aorta
48	chr4:129939400-129942200	Weak transcription	Gastric	stomach
49	chr4:129939400-129942200	Weak transcription	Lung	lung
50	chr4:129939400-129942600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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