Variant report

Variant	rs2589504
Chromosome Location	chr4:86917655-86917656
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11724681	1.00[CEU][hapmap];0.97[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs168308	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs173201	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs182961	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2164535	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2164536	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2164537	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2575680	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2589509	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2665877	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs346467	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs346471	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs346475	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs346478	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs346480	0.94[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs346484	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs346485	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs346488	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs346492	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs346498	0.83[CEU][hapmap];0.81[MEX][hapmap]
rs346502	0.91[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs346503	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs346504	0.86[CEU][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs346505	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs346506	0.91[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs346507	0.91[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35158998	0.84[AMR][1000 genomes]
rs6851229	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs958860	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs958861	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879520	chr4:86829529-86918232	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv1009622	chr4:86893536-87119153	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1005257	chr4:86899596-86925469	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86888800-86919200	Weak transcription	Colon Smooth Muscle	Colon
2	chr4:86889400-86935000	Weak transcription	Psoas Muscle	Psoas
3	chr4:86899200-86927000	Weak transcription	Lung	lung
4	chr4:86899800-86917800	Weak transcription	Small Intestine	intestine
5	chr4:86911000-86919400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr4:86913000-86918200	Strong transcription	Primary B cells from peripheral blood	blood
7	chr4:86913200-86919000	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr4:86914200-86924000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr4:86914400-86917800	Strong transcription	Fetal Muscle Leg	muscle
10	chr4:86914600-86917800	Strong transcription	NHDF-Ad	bronchial
11	chr4:86914800-86918400	Strong transcription	Fetal Muscle Trunk	muscle
12	chr4:86914800-86923200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr4:86915200-86918000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr4:86915200-86918200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr4:86915600-86917800	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr4:86915600-86918200	Strong transcription	Primary B cells from cord blood	blood
17	chr4:86915800-86918000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr4:86915800-86918000	Strong transcription	Muscle Satellite Cultured Cells	--
19	chr4:86915800-86918200	Strong transcription	Fetal Kidney	kidney
20	chr4:86916200-86918600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr4:86916600-86918400	Weak transcription	Brain Hippocampus Middle	brain
22	chr4:86916600-86923600	Weak transcription	Fetal Intestine Small	intestine
23	chr4:86916800-86918400	Weak transcription	Duodenum Mucosa	Duodenum
24	chr4:86916800-86918400	Strong transcription	HUVEC	blood vessel
25	chr4:86916800-86921000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr4:86916800-86923200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr4:86916800-86923200	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr4:86916800-86929400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:86916800-86935800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr4:86916800-86985400	Weak transcription	Ovary	ovary
31	chr4:86917000-86918600	Weak transcription	Placenta	Placenta
32	chr4:86917000-86920000	Weak transcription	Aorta	Aorta
33	chr4:86917000-86923400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr4:86917000-86925000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr4:86917000-86926000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr4:86917000-86929000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr4:86917000-86931800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr4:86917000-86931800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr4:86917000-86931800	Weak transcription	Osteobl	bone
40	chr4:86917000-86932000	Weak transcription	NHLF	lung
41	chr4:86917000-86932400	Weak transcription	Fetal Lung	lung
42	chr4:86917000-86932400	Weak transcription	Right Ventricle	heart
43	chr4:86917000-86933800	Weak transcription	Gastric	stomach
44	chr4:86917000-86933800	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr4:86917000-86935200	Weak transcription	Left Ventricle	heart
46	chr4:86917000-86935800	Weak transcription	Spleen	Spleen
47	chr4:86917000-86954000	Weak transcription	Pancreas	Pancrea
48	chr4:86917200-86921800	Weak transcription	HSMMtube	muscle
49	chr4:86917200-86932000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr4:86917400-86920800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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