Variant report

Variant	rs7665638
Chromosome Location	chr4:88259463-88259464
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs11097131	0.87[YRI][hapmap]
rs11734330	0.91[YRI][hapmap];0.81[AFR][1000 genomes]
rs11931674	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11934060	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11939903	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11940002	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11946007	0.81[AFR][1000 genomes]
rs11946391	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11946465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55663915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55878019	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs55879514	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55933669	1.00[AMR][1000 genomes]
rs55968517	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55974821	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56113853	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56196275	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56293231	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56336118	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57088507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57743836	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57806008	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57948983	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58637341	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs58985971	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59037460	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59137232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59157345	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59311794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59476561	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59593300	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60371489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60404847	0.85[AMR][1000 genomes]
rs60661283	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60690297	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60955120	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61262236	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61367052	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61514672	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs61594871	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61646372	0.91[AFR][1000 genomes]
rs6820688	0.86[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73839181	0.85[AMR][1000 genomes]
rs73839185	1.00[AMR][1000 genomes]
rs73839189	1.00[AMR][1000 genomes]
rs73839191	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73839192	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73841125	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73841126	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73841128	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73841136	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73841139	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73841140	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73841141	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73841142	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73841143	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73841144	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73841145	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7660178	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7671726	0.85[AMR][1000 genomes]
rs7698406	0.86[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997750	chr4:87933945-88264127	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv870296	chr4:88173534-88295927	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1004518	chr4:88218473-88354403	Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv4412	chr4:88237813-88283368	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv1002789	chr4:88239340-88606485	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88253800-88274600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr4:88254800-88260200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr4:88254800-88266000	Weak transcription	Brain Angular Gyrus	brain
4	chr4:88254800-88266000	Weak transcription	Fetal Kidney	kidney
5	chr4:88254800-88311800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr4:88255000-88260200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr4:88255000-88260600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr4:88255000-88263000	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr4:88255000-88263200	Weak transcription	HSMM	muscle
10	chr4:88255000-88266000	Weak transcription	Brain Cingulate Gyrus	brain
11	chr4:88255000-88268200	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr4:88255000-88292400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr4:88255200-88267800	Strong transcription	Duodenum Mucosa	Duodenum
14	chr4:88255200-88274400	Weak transcription	GM12878-XiMat	blood
15	chr4:88255200-88285600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr4:88255200-88293800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr4:88255400-88259600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr4:88255400-88261000	Strong transcription	Fetal Lung	lung
19	chr4:88255400-88263200	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr4:88255400-88264600	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr4:88255600-88266200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr4:88255800-88266200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr4:88255800-88278200	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr4:88256000-88260000	Weak transcription	K562	blood
25	chr4:88256000-88260200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr4:88256000-88260600	Weak transcription	Psoas Muscle	Psoas
27	chr4:88256000-88260600	Weak transcription	Thymus	Thymus
28	chr4:88256000-88262400	Weak transcription	Lung	lung
29	chr4:88256000-88262400	Weak transcription	Spleen	Spleen
30	chr4:88256000-88263000	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr4:88256000-88263000	Strong transcription	Placenta	Placenta
32	chr4:88256000-88265800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr4:88256000-88265800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr4:88256000-88266000	Weak transcription	Brain Hippocampus Middle	brain
35	chr4:88256000-88266200	Weak transcription	Aorta	Aorta
36	chr4:88256000-88274800	Weak transcription	A549	lung
37	chr4:88256200-88260000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr4:88256200-88260600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr4:88256200-88262400	Weak transcription	Pancreas	Pancrea
40	chr4:88256200-88263000	Strong transcription	Liver	Liver
41	chr4:88256200-88265800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr4:88256200-88265800	Weak transcription	Brain Anterior Caudate	brain
43	chr4:88256200-88266000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr4:88256200-88266800	Weak transcription	NHLF	lung
45	chr4:88256200-88267000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr4:88256200-88267200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr4:88256200-88292800	Weak transcription	Gastric	stomach
48	chr4:88256200-88310600	Weak transcription	Right Ventricle	heart
49	chr4:88256400-88260200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr4:88256400-88262400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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