Variant report

Variant	rs7617401
Chromosome Location	chr3:87029291-87029292
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10514743	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17028628	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1898266	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1898267	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1898268	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1946747	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55854261	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56077607	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56338126	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56346369	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56781488	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57070008	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57383190	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57543641	0.87[ASN][1000 genomes]
rs57604593	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59090592	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59701679	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61594756	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6551256	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6762893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6763484	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6784668	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6788077	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6802660	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72916057	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72916059	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72916062	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72916064	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72916069	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72916081	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72916083	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72916086	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72916091	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72916092	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72916098	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72916100	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72916102	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72918103	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72918106	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72918107	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72918108	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72918113	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72918116	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72918121	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72918124	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72918169	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73844420	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73844421	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73844432	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73844434	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73844442	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73844457	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7627441	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7645797	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7649313	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs959081	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534036	chr3:86967129-87283600	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:86998800-87036000	Weak transcription	Psoas Muscle	Psoas
2	chr3:87007200-87038400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr3:87008000-87032000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:87008000-87034200	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr3:87012600-87032600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:87016200-87039000	Weak transcription	Fetal Stomach	stomach
7	chr3:87016800-87036800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr3:87017000-87029400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr3:87017600-87039000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:87018200-87032600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:87018200-87033600	Weak transcription	A549	lung
12	chr3:87018400-87036400	Weak transcription	Fetal Intestine Large	intestine
13	chr3:87018600-87034200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr3:87019400-87036600	Weak transcription	Fetal Brain Male	brain
15	chr3:87026600-87030000	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:87027000-87029800	Genic enhancers	Osteobl	bone
17	chr3:87027200-87032000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr3:87027400-87030200	Enhancers	Colon Smooth Muscle	Colon
19	chr3:87027600-87031000	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr3:87027600-87032000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:87027800-87029400	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr3:87027800-87031000	Weak transcription	NH-A	brain
23	chr3:87027800-87032000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr3:87027800-87032400	Weak transcription	Fetal Muscle Trunk	muscle
25	chr3:87028000-87029800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:87028000-87029800	Enhancers	NHLF	lung
27	chr3:87028000-87031000	Weak transcription	Adipose Nuclei	Adipose
28	chr3:87028000-87031000	Weak transcription	Fetal Lung	lung
29	chr3:87028000-87031000	Weak transcription	Ovary	ovary
30	chr3:87028000-87031400	Weak transcription	Fetal Muscle Leg	muscle
31	chr3:87028000-87032000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr3:87028000-87032000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr3:87028000-87032000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:87028000-87032000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:87028000-87032000	Weak transcription	Aorta	Aorta
36	chr3:87028000-87033600	Weak transcription	Hela-S3	cervix
37	chr3:87028000-87035600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr3:87028000-87036200	Weak transcription	HMEC	breast
39	chr3:87028200-87029400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr3:87028200-87031000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr3:87028200-87032600	Weak transcription	Placenta	Placenta
42	chr3:87028600-87029400	Enhancers	Muscle Satellite Cultured Cells	--
43	chr3:87028800-87030200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr3:87029000-87029400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:87029000-87031000	Enhancers	HSMMtube	muscle
46	chr3:87029200-87029800	Genic enhancers	NHDF-Ad	bronchial
47	chr3:87029200-87030400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:87029200-87031000	Enhancers	HSMM	muscle

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