Variant report

Variant	rs10889030
Chromosome Location	chr1:57628701-57628702
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10789046	1.00[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10889027	0.81[JPT][hapmap]
rs10889028	0.87[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs10889029	0.87[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10889031	0.94[ASN][1000 genomes]
rs11206990	0.94[ASN][1000 genomes]
rs1504589	0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs155287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs155288	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs155315	0.94[ASN][1000 genomes]
rs155316	0.94[ASN][1000 genomes]
rs1831870	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs197109	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs4912429	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs4912430	0.84[EUR][1000 genomes]
rs4912431	0.84[EUR][1000 genomes]
rs4912432	0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs524370	0.95[ASN][1000 genomes]
rs55944821	0.84[EUR][1000 genomes]
rs624526	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs6680219	0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs6680429	0.95[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs6693209	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7539865	0.90[ASN][1000 genomes]
rs7546422	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7548633	0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs7552759	0.85[EUR][1000 genomes]
rs9970802	0.95[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.94[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	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv461628	chr1:57463326-57816489	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv546305	chr1:57463326-57816489	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57623200-57635400	Weak transcription	Fetal Intestine Small	intestine
2	chr1:57623800-57629000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:57624000-57644800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:57624200-57628800	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr1:57624400-57629000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr1:57626400-57629000	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr1:57626400-57629000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:57627000-57629400	Enhancers	Fetal Brain Male	brain
9	chr1:57627000-57629800	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr1:57627600-57629600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:57627600-57629600	Enhancers	Brain Cingulate Gyrus	brain
12	chr1:57627600-57629600	Enhancers	Brain Hippocampus Middle	brain
13	chr1:57627800-57629200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:57627800-57629200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:57627800-57629200	Enhancers	Brain Angular Gyrus	brain
16	chr1:57627800-57629200	Enhancers	Brain Germinal Matrix	brain
17	chr1:57627800-57629200	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr1:57627800-57629400	Enhancers	Brain Substantia Nigra	brain
19	chr1:57627800-57629600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:57627800-57629600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:57628000-57629200	Enhancers	Pancreas	Pancrea
22	chr1:57628000-57629800	Enhancers	H1 Cell Line	embryonic stem cell
23	chr1:57628000-57629800	Enhancers	Brain Anterior Caudate	brain
24	chr1:57628000-57632000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:57628000-57632000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:57628200-57628800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:57628200-57628800	Enhancers	Fetal Brain Female	brain
28	chr1:57628200-57631400	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr1:57628400-57629000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:57628600-57628800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr1:57628600-57628800	Enhancers	Small Intestine	intestine
32	chr1:57628600-57629200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr1:57628600-57629400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:57628600-57629400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr1:57628600-57629400	Enhancers	Left Ventricle	heart
36	chr1:57628600-57629600	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr1:57628600-57629600	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr1:57628600-57629800	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr1:57628600-57629800	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr1:57628600-57630400	Enhancers	ES-WA7 Cell Line	embryonic stem cell

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