Variant report

Variant	rs563740
Chromosome Location	chr7:69168149-69168150
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1008379	0.80[ASN][1000 genomes]
rs10085775	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1014382	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10237145	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10241485	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11765886	0.94[ASN][1000 genomes]
rs12333508	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12698812	0.83[ASN][1000 genomes]
rs12698814	0.83[ASN][1000 genomes]
rs12698815	0.87[ASN][1000 genomes]
rs12698820	0.81[ASN][1000 genomes]
rs13232095	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs13236841	0.85[ASN][1000 genomes]
rs1468588	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17353815	0.89[ASN][1000 genomes]
rs17458097	0.88[ASN][1000 genomes]
rs2058395	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs210598	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs210600	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs210603	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2159679	0.80[ASN][1000 genomes]
rs2253711	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2533432	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2533434	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2533440	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2533446	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2533447	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2533449	0.87[EUR][1000 genomes]
rs2851485	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2851488	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2851500	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2851504	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2851509	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2851512	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2851517	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4717521	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs521259	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs588004	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60739014	0.94[ASN][1000 genomes]
rs608796	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs611052	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs611573	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs622767	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs624626	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6460528	0.89[ASN][1000 genomes]
rs674865	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6955815	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6957302	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6959766	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6974004	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs720056	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs763759	0.88[ASN][1000 genomes]
rs7781403	0.94[ASN][1000 genomes]
rs7793984	0.96[ASN][1000 genomes]
rs7808773	0.80[ASN][1000 genomes]
rs917616	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9638575	0.87[ASN][1000 genomes]
rs981291	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs988282	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]

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	nsv916011	chr7:68942155-69330800	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv428169	chr7:69021482-69196743	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv831021	chr7:69122169-69364491	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1021538	chr7:69130236-69575753	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv538917	chr7:69130236-69575753	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv817276	chr7:69130237-69736834	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1034380	chr7:69137914-69171449	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
8	nsv1018749	chr7:69149029-69995112	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:69161400-69171000	Weak transcription	Left Ventricle	heart
2	chr7:69161400-69171200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:69161600-69173400	Weak transcription	Right Atrium	heart
4	chr7:69161800-69170400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr7:69162000-69186200	Weak transcription	Primary B cells from cord blood	blood
6	chr7:69162200-69170800	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr7:69162600-69168800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr7:69163600-69174000	Weak transcription	Fetal Thymus	thymus
9	chr7:69163800-69171000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr7:69165000-69168400	Enhancers	Fetal Brain Female	brain
11	chr7:69165400-69169200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr7:69166000-69168600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr7:69166200-69169200	Enhancers	Brain Hippocampus Middle	brain
14	chr7:69166400-69168600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr7:69166400-69168600	Enhancers	Brain Angular Gyrus	brain
16	chr7:69166400-69169200	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr7:69166600-69169000	Enhancers	Brain Cingulate Gyrus	brain
18	chr7:69166600-69175400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr7:69166800-69168400	Enhancers	Dnd41	blood
20	chr7:69166800-69168600	Enhancers	Brain Anterior Caudate	brain
21	chr7:69167000-69169200	Enhancers	Ovary	ovary
22	chr7:69167200-69168800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr7:69167400-69168400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr7:69167400-69169200	Enhancers	Colon Smooth Muscle	Colon
25	chr7:69167400-69171000	Weak transcription	Fetal Brain Male	brain
26	chr7:69167600-69168400	Enhancers	Psoas Muscle	Psoas
27	chr7:69167600-69169200	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr7:69167600-69169200	Enhancers	Rectal Smooth Muscle	rectum
29	chr7:69167800-69168200	Weak transcription	Brain Substantia Nigra	brain
30	chr7:69167800-69168400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr7:69167800-69168600	Enhancers	Fetal Stomach	stomach
32	chr7:69167800-69168800	Enhancers	Brain Germinal Matrix	brain
33	chr7:69167800-69169000	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr7:69167800-69169000	Enhancers	Fetal Lung	lung
35	chr7:69167800-69169200	Enhancers	Stomach Smooth Muscle	stomach
36	chr7:69168000-69168200	Enhancers	Gastric	stomach
37	chr7:69168000-69168200	Enhancers	Lung	lung
38	chr7:69168000-69168200	Flanking Active TSS	GM12878-XiMat	blood
39	chr7:69168000-69168400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr7:69168000-69168800	Enhancers	Fetal Heart	heart
41	chr7:69168000-69169200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr7:69168000-69169200	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr7:69168000-69173000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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