Variant report

Variant	rs1360143
Chromosome Location	chr1:196576364-196576365
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10737671	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10737676	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10737678	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10754192	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10754193	0.88[YRI][hapmap]
rs10754194	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10754197	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10801536	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10922081	1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs10922087	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12072649	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133987	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1339947	1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs1339949	0.86[EUR][1000 genomes]
rs1339951	1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs1416960	0.87[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1416966	1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs1416970	1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs1416971	0.85[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs1538683	0.87[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1556961	1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs1571489	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16839886	1.00[JPT][hapmap]
rs16839905	1.00[JPT][hapmap]
rs16839906	1.00[JPT][hapmap]
rs16839910	1.00[JPT][hapmap]
rs16839919	1.00[JPT][hapmap]
rs16840397	1.00[JPT][hapmap]
rs2335906	0.88[YRI][hapmap]
rs2335907	1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs4294368	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4314834	0.92[YRI][hapmap];0.83[AFR][1000 genomes]
rs4316314	1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs4405100	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4515738	0.92[YRI][hapmap];0.83[AFR][1000 genomes]
rs4518841	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4562566	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4601531	0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4614205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4625226	0.92[YRI][hapmap]
rs4633231	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4658040	0.91[YRI][hapmap];0.83[AFR][1000 genomes]
rs4658042	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4658043	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs479718	1.00[JPT][hapmap]
rs6663649	0.88[YRI][hapmap]
rs6670223	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6675592	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6680722	0.86[EUR][1000 genomes]
rs6680890	0.83[AFR][1000 genomes]
rs6688468	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6702610	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7531491	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7533533	0.88[YRI][hapmap];0.83[AFR][1000 genomes]
rs7540922	0.88[YRI][hapmap];0.83[AFR][1000 genomes]
rs7541165	0.82[EUR][1000 genomes]
rs7544266	1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs7552170	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[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	nsv931415	chr1:196270759-196744780	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv528460	chr1:196542567-197446702	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv947214	chr1:196573327-196578627	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:196573400-196576600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr1:196573400-196577000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr1:196574600-196576800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:196574800-196578600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr1:196574800-196578800	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr1:196575200-196576600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr1:196575400-196576400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:196575400-196576600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr1:196575800-196576400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr1:196575800-196576600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr1:196575800-196576600	Enhancers	Fetal Kidney	kidney
12	chr1:196575800-196577000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:196575800-196578200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:196575800-196578400	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr1:196575800-196578600	Active TSS	H1 Cell Line	embryonic stem cell
16	chr1:196575800-196579200	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr1:196576000-196576400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr1:196576000-196576600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:196576000-196576800	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr1:196576000-196578600	Active TSS	Ovary	ovary
21	chr1:196576000-196578600	Active TSS	Right Atrium	heart
22	chr1:196576200-196576400	Active TSS	Aorta	Aorta
23	chr1:196576200-196576400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
24	chr1:196576200-196576400	Enhancers	Fetal Stomach	stomach
25	chr1:196576200-196576800	Active TSS	Fetal Brain Female	brain
26	chr1:196576200-196578000	Active TSS	Liver	Liver
27	chr1:196576200-196578400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:196576200-196578400	Active TSS	Brain Inferior Temporal Lobe	brain
29	chr1:196576200-196578400	Active TSS	Fetal Brain Male	brain
30	chr1:196576200-196578600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr1:196576200-196578800	Active TSS	H9 Cell Line	embryonic stem cell

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