Variant report

Variant	rs2474123
Chromosome Location	chr1:85827452-85827453
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1001604	0.89[CEU][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes]
rs10489513	0.89[CEU][hapmap];0.81[MKK][hapmap];0.85[AMR][1000 genomes]
rs11161606	0.82[ASW][hapmap];0.85[CEU][hapmap];0.92[GIH][hapmap];0.82[LWK][hapmap];0.84[MEX][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11161609	0.81[ASN][1000 genomes]
rs1146382	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12044537	0.88[CEU][hapmap];0.85[AMR][1000 genomes]
rs1240939	0.89[ASN][1000 genomes]
rs1498373	0.82[CEU][hapmap]
rs18582	0.82[CEU][hapmap];0.84[MEX][hapmap]
rs2268667	0.82[CEU][hapmap]
rs2300634	0.82[CEU][hapmap]
rs233047	0.82[CEU][hapmap]
rs233053	0.88[CEU][hapmap];0.81[MKK][hapmap];0.87[AMR][1000 genomes]
rs233061	0.81[EUR][1000 genomes]
rs233068	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs233072	0.92[CEU][hapmap];0.89[MEX][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs233093	0.82[CEU][hapmap];0.84[MEX][hapmap]
rs233097	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs233099	0.82[CEU][hapmap];0.84[MEX][hapmap]
rs233109	0.81[EUR][1000 genomes]
rs233112	0.92[CEU][hapmap];0.83[MEX][hapmap];0.80[EUR][1000 genomes]
rs233113	0.82[CEU][hapmap]
rs233115	0.80[CEU][hapmap]
rs233118	0.92[CEU][hapmap];0.84[MEX][hapmap];0.81[EUR][1000 genomes]
rs233119	0.82[CEU][hapmap]
rs233124	0.92[CEU][hapmap];0.84[MEX][hapmap];0.81[EUR][1000 genomes]
rs233130	0.92[CEU][hapmap]
rs233133	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2840319	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3768227	0.82[CEU][hapmap];0.84[MEX][hapmap]
rs3920521	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs530006	0.83[GIH][hapmap]
rs591917	0.86[CHB][hapmap]
rs648216	0.81[CHB][hapmap]
rs6576761	0.81[EUR][1000 genomes]
rs6576763	0.82[ASW][hapmap];0.89[CEU][hapmap];0.81[MKK][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes]
rs6576765	0.89[CEU][hapmap];0.81[MKK][hapmap];0.82[AMR][1000 genomes]
rs6576766	0.83[AMR][1000 genomes]
rs661686	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6697083	0.81[CEU][hapmap];0.84[JPT][hapmap]
rs729655	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7521189	0.83[GIH][hapmap]
rs7525786	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7547571	0.83[EUR][1000 genomes]
rs761601	0.82[CEU][hapmap];0.84[MEX][hapmap]

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	nsv830470	chr1:85820775-86014080	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85809200-85838400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:85809600-85828800	Weak transcription	Brain Anterior Caudate	brain
3	chr1:85814200-85839600	Weak transcription	Left Ventricle	heart
4	chr1:85816000-85831400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:85816000-85839600	Weak transcription	Pancreas	Pancrea
6	chr1:85816400-85829000	Weak transcription	Stomach Smooth Muscle	stomach
7	chr1:85816600-85836800	Weak transcription	Fetal Muscle Trunk	muscle
8	chr1:85823200-85836800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr1:85824400-85833800	Weak transcription	Fetal Intestine Small	intestine
10	chr1:85824600-85827600	Enhancers	A549	lung
11	chr1:85824600-85829600	Enhancers	NHLF	lung
12	chr1:85824800-85827600	Enhancers	HSMMtube	muscle
13	chr1:85824800-85827600	Enhancers	NH-A	brain
14	chr1:85824800-85828400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:85825000-85839000	Weak transcription	Aorta	Aorta
16	chr1:85825200-85828800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:85825200-85828800	Weak transcription	Psoas Muscle	Psoas
18	chr1:85825200-85830400	Enhancers	Osteobl	bone
19	chr1:85825400-85828000	Enhancers	Colon Smooth Muscle	Colon
20	chr1:85825400-85829600	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr1:85825600-85829600	Enhancers	Fetal Lung	lung
22	chr1:85825800-85829000	Enhancers	HSMM	muscle
23	chr1:85826200-85827600	Enhancers	HepG2	liver
24	chr1:85826200-85828000	Weak transcription	Brain Cingulate Gyrus	brain
25	chr1:85826200-85832000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:85826200-85838800	Weak transcription	Hela-S3	cervix
27	chr1:85826400-85831200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:85826600-85827600	Enhancers	Fetal Kidney	kidney
29	chr1:85826600-85827600	Enhancers	Stomach Mucosa	stomach
30	chr1:85826800-85827600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr1:85826800-85827600	Enhancers	Small Intestine	intestine
32	chr1:85826800-85828000	Weak transcription	Fetal Brain Male	brain
33	chr1:85826800-85829000	Weak transcription	Fetal Brain Female	brain
34	chr1:85826800-85829600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:85826800-85829800	Enhancers	Fetal Stomach	stomach
36	chr1:85826800-85830000	Enhancers	Muscle Satellite Cultured Cells	--
37	chr1:85826800-85831000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr1:85827000-85828000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr1:85827000-85828200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr1:85827000-85833800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr1:85827000-85834600	Enhancers	NHDF-Ad	bronchial
42	chr1:85827000-85837800	Weak transcription	Rectal Smooth Muscle	rectum
43	chr1:85827200-85828000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr1:85827200-85828000	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr1:85827200-85828000	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr1:85827200-85828800	Weak transcription	Fetal Muscle Leg	muscle
47	chr1:85827200-85831400	Weak transcription	Ovary	ovary
48	chr1:85827200-85831400	Weak transcription	HUVEC	blood vessel
49	chr1:85827200-85832200	Weak transcription	HMEC	breast
50	chr1:85827200-85836800	Weak transcription	Adipose Nuclei	Adipose

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