Variant report

Variant	rs4949889
Chromosome Location	chr1:85778344-85778345
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1006989	0.82[EUR][1000 genomes]
rs10489510	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10747318	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10782549	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10873701	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12022248	0.91[ASN][1000 genomes]
rs12029221	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12033483	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12034249	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12035116	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12038426	0.91[AFR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12042780	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12047189	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1261681	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1342323	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1357635	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1357636	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1391556	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1523995	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1608537	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17384213	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17388696	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1965876	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2016104	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2037594	0.82[EUR][1000 genomes]
rs2064510	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2124139	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2300633	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2389948	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3851268	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4428939	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4512701	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4631749	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4949897	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4949898	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4949899	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs499869	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs539714	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs600098	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs604974	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs631817	0.82[EUR][1000 genomes]
rs6420965	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs659070	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6672870	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72722663	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72722671	0.99[ASN][1000 genomes]
rs72722691	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72724608	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs731194	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7515261	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7539738	0.82[EUR][1000 genomes]
rs7555670	0.82[EUR][1000 genomes]
rs990916	0.92[EUR][1000 genomes];0.84[ASN][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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv830459	chr1:85589585-85786311	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85772800-85779800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:85774000-85779600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:85774400-85779400	Weak transcription	Aorta	Aorta
4	chr1:85774600-85779000	Weak transcription	Fetal Heart	heart
5	chr1:85774600-85779000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr1:85774600-85779400	Weak transcription	Colon Smooth Muscle	Colon
7	chr1:85774600-85779600	Weak transcription	Fetal Lung	lung
8	chr1:85774600-85779600	Weak transcription	Ovary	ovary
9	chr1:85774600-85779800	Weak transcription	Placenta	Placenta
10	chr1:85774600-85779800	Weak transcription	Right Atrium	heart
11	chr1:85774600-85780000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:85774600-85780000	Weak transcription	Lung	lung
13	chr1:85774600-85780000	Weak transcription	Pancreas	Pancrea
14	chr1:85774600-85780000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr1:85774600-85780000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr1:85774600-85782400	Weak transcription	Fetal Intestine Small	intestine
17	chr1:85774600-85785200	Weak transcription	Liver	Liver
18	chr1:85774600-85785800	Weak transcription	Fetal Intestine Large	intestine
19	chr1:85774600-85787000	Weak transcription	Fetal Stomach	stomach
20	chr1:85774600-85794800	Weak transcription	Spleen	Spleen
21	chr1:85774800-85779000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:85774800-85779600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr1:85774800-85782200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:85774800-85782200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr1:85774800-85784000	Weak transcription	HepG2	liver
26	chr1:85774800-85790400	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr1:85774800-85790600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr1:85774800-85794200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:85775000-85779600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:85775000-85781400	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr1:85775400-85779400	Weak transcription	A549	lung
32	chr1:85777200-85779200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:85777200-85781400	Weak transcription	Brain Germinal Matrix	brain
34	chr1:85777400-85778400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:85777400-85778400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:85777400-85778400	Enhancers	HSMMtube	muscle
37	chr1:85777400-85779000	Enhancers	Muscle Satellite Cultured Cells	--
38	chr1:85777400-85781600	Enhancers	Osteobl	bone
39	chr1:85777400-85786400	Enhancers	NHLF	lung
40	chr1:85777600-85778400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:85777600-85778400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:85777600-85780000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:85777600-85782400	Enhancers	HUVEC	blood vessel
44	chr1:85777600-85784000	Enhancers	NHDF-Ad	bronchial
45	chr1:85777800-85778400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:85777800-85778400	Enhancers	NHEK	skin
47	chr1:85777800-85782800	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr1:85778000-85779000	Weak transcription	Left Ventricle	heart
49	chr1:85778000-85779000	Weak transcription	Psoas Muscle	Psoas
50	chr1:85778000-85780000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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