Variant report

Variant	rs1999945
Chromosome Location	chr7:86593390-86593391
allele	C/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:40)

rs_ID	r²[population]
rs10215436	0.81[EUR][1000 genomes]
rs10238192	1.00[JPT][hapmap]
rs10250697	1.00[JPT][hapmap]
rs10253313	1.00[JPT][hapmap]
rs10263372	1.00[CHB][hapmap];0.90[TSI][hapmap]
rs10275872	1.00[JPT][hapmap]
rs12111888	1.00[CHB][hapmap]
rs17161067	1.00[CHB][hapmap]
rs17161098	1.00[CHB][hapmap]
rs17161118	1.00[CHB][hapmap];0.91[YRI][hapmap];0.83[EUR][1000 genomes]
rs17697878	0.87[CEU][hapmap]
rs1999946	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1999947	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59352637	0.83[ASN][1000 genomes]
rs60623709	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61699848	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6465087	0.85[CEU][hapmap]
rs6465089	0.85[CEU][hapmap]
rs6947778	0.85[CEU][hapmap]
rs6954573	0.85[CEU][hapmap]
rs6955452	0.85[CEU][hapmap]
rs6955565	0.85[CEU][hapmap]
rs6955917	0.85[CEU][hapmap]
rs6957842	0.85[CEU][hapmap]
rs6960053	0.85[CEU][hapmap]
rs6967992	0.85[CEU][hapmap]
rs6972489	1.00[CHB][hapmap]
rs6974507	0.85[CEU][hapmap]
rs6978155	0.85[CEU][hapmap]
rs73384105	0.83[AFR][1000 genomes]
rs73384108	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73384109	0.92[EUR][1000 genomes]
rs73384111	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73384112	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73384113	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73384121	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7781782	1.00[CHB][hapmap];0.84[GIH][hapmap];0.90[TSI][hapmap]
rs7781922	0.85[CEU][hapmap]
rs7801050	0.85[CEU][hapmap];0.82[YRI][hapmap]
rs7808623	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025032	chr7:86032479-86642973	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv1025277	chr7:86299224-87206007	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv538999	chr7:86299224-87206007	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
4	nsv532147	chr7:86299225-87121975	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv1015870	chr7:86490491-86802320	Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
6	nsv539000	chr7:86490491-86802320	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
7	nsv527889	chr7:86496042-86832603	Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv525634	chr7:86590353-86608786	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:86579200-86594400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr7:86580200-86596000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr7:86588000-86594200	Weak transcription	Pancreas	Pancrea
4	chr7:86589800-86605800	Weak transcription	Aorta	Aorta
5	chr7:86590800-86593400	Enhancers	Brain Cingulate Gyrus	brain
6	chr7:86591000-86593400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr7:86591200-86593400	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr7:86591200-86595600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr7:86591400-86594200	Enhancers	Brain Anterior Caudate	brain
10	chr7:86591400-86596400	Weak transcription	Lung	lung
11	chr7:86591800-86593600	Enhancers	Fetal Heart	heart
12	chr7:86591800-86597200	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr7:86592400-86593400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr7:86592400-86598600	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr7:86592600-86593400	Flanking Active TSS	Brain Hippocampus Middle	brain
16	chr7:86592600-86593400	Enhancers	GM12878-XiMat	blood
17	chr7:86592600-86593600	Enhancers	NHDF-Ad	bronchial
18	chr7:86592600-86594000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr7:86592800-86593400	Enhancers	Pancreatic Islets	Pancreatic Islet
20	chr7:86592800-86593600	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr7:86592800-86595600	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr7:86592800-86596000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr7:86592800-86596400	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr7:86592800-86596400	Weak transcription	Gastric	stomach
25	chr7:86593000-86593400	Enhancers	K562	blood
26	chr7:86593000-86595600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr7:86593000-86596200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr7:86593000-86597200	Weak transcription	Brain Germinal Matrix	brain
29	chr7:86593000-86598400	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr7:86593000-86598600	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr7:86593200-86593400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr7:86593200-86593400	Active TSS	Brain Angular Gyrus	brain
33	chr7:86593200-86593400	Enhancers	Brain Substantia Nigra	brain
34	chr7:86593200-86593600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr7:86593200-86594200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr7:86593200-86594200	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr7:86593200-86594200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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