Variant report

Variant	rs2390539
Chromosome Location	chr7:21544345-21544346
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1013716	0.85[CHB][hapmap]
rs10269168	0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10272006	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11971316	1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11983472	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12668354	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12672629	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12673975	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2158414	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2237303	0.84[CEU][hapmap]
rs2282888	0.88[CEU][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28541530	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3735440	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs39298	0.85[CHB][hapmap]
rs40245	0.85[JPT][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs41495348	0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4397283	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4722031	0.89[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4722033	0.86[AMR][1000 genomes]
rs6461561	0.82[JPT][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes]
rs6461562	1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs6461565	0.85[CHB][hapmap]
rs6461568	1.00[CEU][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6948810	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6974974	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6978922	0.85[ASN][1000 genomes]
rs7780553	0.80[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7781732	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7792280	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs7796796	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7798894	1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7802314	0.84[CEU][hapmap]
rs7810841	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9639377	0.84[CEU][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9639378	0.88[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027302	chr7:21391598-21727016	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv538800	chr7:21391598-21727016	Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1028434	chr7:21468437-21636671	ZNF genes & repeats Strong transcription Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv1023655	chr7:21486485-21727016	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv538801	chr7:21486485-21727016	ZNF genes & repeats Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv830921	chr7:21489100-21688016	Strong transcription ZNF genes & repeats Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:21487400-21557000	Weak transcription	Aorta	Aorta
2	chr7:21492200-21545200	Weak transcription	Small Intestine	intestine
3	chr7:21500000-21552800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr7:21516200-21556400	Weak transcription	Brain Substantia Nigra	brain
5	chr7:21517000-21556000	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr7:21520800-21552800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr7:21521200-21552600	Weak transcription	Brain Angular Gyrus	brain
8	chr7:21531400-21544400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr7:21533200-21547600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr7:21533400-21550400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr7:21533600-21549800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr7:21536600-21549400	Weak transcription	Left Ventricle	heart
13	chr7:21536600-21550000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr7:21536600-21550600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr7:21536600-21557000	Weak transcription	Psoas Muscle	Psoas
16	chr7:21536800-21550800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr7:21536800-21550800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr7:21536800-21552800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr7:21537000-21547800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr7:21537400-21549000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr7:21538800-21555000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr7:21539200-21552600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr7:21539600-21554800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr7:21539600-21555800	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr7:21539800-21551600	Strong transcription	Primary B cells from cord blood	blood
26	chr7:21540200-21544600	Strong transcription	Ovary	ovary
27	chr7:21540600-21550800	Weak transcription	Fetal Lung	lung
28	chr7:21540600-21551600	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr7:21540600-21554400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr7:21540800-21545200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr7:21540800-21551400	Weak transcription	Brain Anterior Caudate	brain
32	chr7:21541000-21554800	Weak transcription	Lung	lung
33	chr7:21541600-21547000	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr7:21541600-21547800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
35	chr7:21542000-21544400	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr7:21542000-21551200	Weak transcription	Fetal Kidney	kidney
37	chr7:21542200-21546600	Weak transcription	Fetal Heart	heart
38	chr7:21542200-21547400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr7:21542200-21547600	Weak transcription	Fetal Muscle Leg	muscle
40	chr7:21542200-21548200	Weak transcription	Fetal Muscle Trunk	muscle
41	chr7:21542200-21552200	Weak transcription	Adipose Nuclei	Adipose
42	chr7:21542400-21544400	Weak transcription	Thymus	Thymus
43	chr7:21542400-21546800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr7:21542800-21547400	Weak transcription	Fetal Stomach	stomach
45	chr7:21543000-21544400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr7:21543000-21544600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
47	chr7:21543000-21545600	ZNF genes & repeats	Primary T cells from cord blood	blood
48	chr7:21543400-21545000	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr7:21543400-21548000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr7:21543600-21544600	Weak transcription	Primary B cells from peripheral blood	blood

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