Variant report

Variant	rs1399618
Chromosome Location	chr11:83952285-83952286
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:83941713..83944829-chr11:83950244..83953336,4	MCF-7	breast:
2	chr11:83951528..83953158-chr11:83957231..83960545,3	MCF-7	breast:

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10128587	0.95[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs1022308	0.95[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.96[ASN][1000 genomes]
rs1040131	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10751105	0.94[JPT][hapmap]
rs10751106	0.94[JPT][hapmap]
rs10751109	1.00[JPT][hapmap]
rs10751112	0.97[ASN][1000 genomes]
rs10792727	0.88[JPT][hapmap]
rs10792731	0.94[JPT][hapmap]
rs10792740	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.97[ASN][1000 genomes]
rs10792742	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10792744	0.95[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[ASN][1000 genomes]
rs10792745	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10792746	0.95[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap];0.86[ASN][1000 genomes]
rs10898214	0.85[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10898215	0.95[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.97[ASN][1000 genomes]
rs10898216	0.97[ASN][1000 genomes]
rs10898217	0.97[ASN][1000 genomes]
rs10898218	0.97[ASN][1000 genomes]
rs10898219	0.97[ASN][1000 genomes]
rs10898222	1.00[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs11233953	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11233954	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[ASN][1000 genomes]
rs11233956	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11233963	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11233967	0.95[CHB][hapmap];0.91[ASN][1000 genomes]
rs12278134	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[ASN][1000 genomes]
rs12281587	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1349820	0.94[JPT][hapmap]
rs1377746	0.89[JPT][hapmap]
rs1377747	0.89[JPT][hapmap]
rs1377748	0.94[JPT][hapmap]
rs1399617	0.88[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1454021	0.82[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1454023	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.87[MEX][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1454026	0.94[JPT][hapmap]
rs1515084	0.95[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs1515091	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1515092	1.00[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs1515094	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1573572	0.88[JPT][hapmap]
rs1793037	0.89[JPT][hapmap]
rs1793039	0.83[JPT][hapmap]
rs1849877	0.80[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1869470	0.84[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1869471	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1869472	0.88[JPT][hapmap]
rs1901973	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2156848	0.94[JPT][hapmap]
rs2374526	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4354715	0.95[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs4943889	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4944471	0.94[JPT][hapmap]
rs4944472	0.94[JPT][hapmap]
rs4944474	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7103429	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7106175	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7112322	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs7122248	0.95[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs7130225	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73519747	0.97[ASN][1000 genomes]
rs7483548	1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap];0.89[ASN][1000 genomes]
rs7925243	0.95[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.95[ASN][1000 genomes]
rs7933566	0.90[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.92[ASN][1000 genomes]
rs7937925	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[ASN][1000 genomes]
rs7941004	0.94[JPT][hapmap]
rs7943267	0.89[JPT][hapmap]
rs896996	0.80[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs896997	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs896998	0.92[ASN][1000 genomes]
rs930790	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs963259	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs988322	0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039924	chr11:83662904-83993497	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv541102	chr11:83662904-83993497	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv948410	chr11:83918339-84812001	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv415	chr11:83924941-83969603	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:83945400-83961200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr11:83945800-83957400	Weak transcription	Brain Angular Gyrus	brain
3	chr11:83946200-83952800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr11:83946200-83953000	Weak transcription	Brain Hippocampus Middle	brain
5	chr11:83946400-83952600	Weak transcription	Brain Anterior Caudate	brain
6	chr11:83946600-83952400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr11:83951200-83953400	Enhancers	Fetal Intestine Large	intestine
8	chr11:83951800-83952400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr11:83951800-83952800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr11:83951800-83953400	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr11:83952000-83952400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
12	chr11:83952000-83952400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr11:83952000-83953200	Enhancers	H1 Cell Line	embryonic stem cell
14	chr11:83952000-83953200	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr11:83952000-83953200	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr11:83952000-83953200	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr11:83952000-83953400	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr11:83952000-83953400	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr11:83952000-83953400	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr11:83952000-83953400	Enhancers	Liver	Liver
21	chr11:83952200-83952800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr11:83952200-83953000	Weak transcription	Brain Substantia Nigra	brain

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