Variant report

Variant	rs59378342
Chromosome Location	chr9:3320190-3320191
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 129 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs10429463	0.89[EUR][1000 genomes]
rs11998979	0.81[EUR][1000 genomes]
rs13284120	0.89[ASN][1000 genomes]
rs13296552	0.89[ASN][1000 genomes]
rs16916423	0.86[EUR][1000 genomes]
rs17658724	0.88[EUR][1000 genomes]
rs17715160	0.84[EUR][1000 genomes]
rs17715317	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17715329	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2274487	0.95[ASN][1000 genomes]
rs2304928	0.86[EUR][1000 genomes]
rs2920363	0.81[EUR][1000 genomes]
rs2920364	0.90[ASN][1000 genomes]
rs2920366	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2920368	0.89[ASN][1000 genomes]
rs2920369	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2920370	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2920376	0.90[ASN][1000 genomes]
rs2920377	0.89[ASN][1000 genomes]
rs2920378	0.90[ASN][1000 genomes]
rs2920379	0.90[ASN][1000 genomes]
rs2920380	0.90[ASN][1000 genomes]
rs2920381	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2920382	0.85[ASN][1000 genomes]
rs2920383	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2986678	0.86[ASN][1000 genomes]
rs2986679	0.89[ASN][1000 genomes]
rs2986680	0.90[ASN][1000 genomes]
rs2986686	0.91[EUR][1000 genomes]
rs2986687	0.86[EUR][1000 genomes]
rs2986688	0.85[ASN][1000 genomes]
rs2986690	0.83[ASN][1000 genomes]
rs2986691	0.88[ASN][1000 genomes]
rs2986693	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2986694	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2986695	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2986696	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2986697	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2986698	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2986699	0.86[ASN][1000 genomes]
rs2986700	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2986701	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2986702	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2986703	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2991300	0.82[EUR][1000 genomes]
rs2991301	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2991302	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2991304	0.95[ASN][1000 genomes]
rs2991305	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2991306	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2991307	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2991308	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2991309	0.89[ASN][1000 genomes]
rs2991310	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2991311	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2991314	0.90[ASN][1000 genomes]
rs2991315	0.90[ASN][1000 genomes]
rs2991316	0.92[ASN][1000 genomes]
rs2991317	0.89[ASN][1000 genomes]
rs2991318	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2991319	0.89[ASN][1000 genomes]
rs2991320	0.87[ASN][1000 genomes]
rs2991321	0.87[ASN][1000 genomes]
rs2991323	0.85[ASN][1000 genomes]
rs3012670	0.87[ASN][1000 genomes]
rs3012672	0.87[ASN][1000 genomes]
rs3012686	0.81[EUR][1000 genomes]
rs3012688	0.81[EUR][1000 genomes]
rs3012692	0.81[ASN][1000 genomes]
rs3012693	0.88[EUR][1000 genomes]
rs3012694	0.86[ASN][1000 genomes]
rs3012695	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3012696	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3012697	0.84[ASN][1000 genomes]
rs3012700	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3012701	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3012702	0.90[ASN][1000 genomes]
rs3012705	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3012706	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3012707	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3012708	0.95[ASN][1000 genomes]
rs3012709	0.95[ASN][1000 genomes]
rs3012710	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3012711	0.95[ASN][1000 genomes]
rs3012712	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3012713	0.85[ASN][1000 genomes]
rs4008965	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41312820	0.81[EUR][1000 genomes]
rs4495486	0.95[ASN][1000 genomes]
rs57295144	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs576347	0.83[EUR][1000 genomes]
rs58010475	0.89[EUR][1000 genomes]
rs617992	0.84[EUR][1000 genomes]
rs66573713	0.85[ASN][1000 genomes]
rs7025201	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7025328	0.90[EUR][1000 genomes]
rs7035429	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7044448	0.93[EUR][1000 genomes]
rs72699004	0.85[EUR][1000 genomes]
rs72699014	0.85[EUR][1000 genomes]
rs72699023	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72699033	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72699037	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72699039	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72699050	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72699051	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72699063	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72699067	0.87[ASN][1000 genomes]
rs72699069	0.87[ASN][1000 genomes]
rs7850653	0.85[ASN][1000 genomes]
rs7850660	0.85[ASN][1000 genomes]
rs7859468	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7860020	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7861667	0.85[ASN][1000 genomes]
rs7861699	0.85[ASN][1000 genomes]
rs7871277	0.85[ASN][1000 genomes]
rs9408234	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892086	chr9:3012276-3410838	Bivalent Enhancer ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1032921	chr9:3139007-3502815	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv539940	chr9:3139007-3502815	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv466090	chr9:3237378-3349487	Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv613145	chr9:3237378-3349487	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv531566	chr9:3288211-3545454	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv892089	chr9:3290569-3578094	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
8	nsv916259	chr9:3308176-4296711	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
9	nsv1034280	chr9:3319718-3491987	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv539942	chr9:3319718-3491987	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv1028815	chr9:3319718-3584455	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
12	esv3383377	chr9:3319802-3322000	Weak transcription Enhancers Strong transcription	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3244200-3338400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr9:3265600-3332000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr9:3277400-3337400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr9:3288200-3378400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr9:3291400-3338600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr9:3293200-3329600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr9:3293600-3352600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr9:3294800-3321200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:3302400-3323600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr9:3305400-3328600	Weak transcription	GM12878-XiMat	blood
11	chr9:3306800-3337400	Weak transcription	Left Ventricle	heart
12	chr9:3307200-3325000	Weak transcription	Pancreas	Pancrea
13	chr9:3308600-3337000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr9:3309400-3350400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr9:3310200-3337000	Weak transcription	Primary B cells from cord blood	blood
16	chr9:3311600-3338800	Weak transcription	Thymus	Thymus
17	chr9:3313200-3337000	Weak transcription	Aorta	Aorta
18	chr9:3313400-3352400	Weak transcription	Primary T cells from cord blood	blood
19	chr9:3318800-3337400	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr9:3319000-3320600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr9:3319000-3347800	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr9:3319600-3330200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr9:3319600-3337200	Weak transcription	Brain Anterior Caudate	brain
24	chr9:3319800-3353800	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr9:3320000-3320600	Strong transcription	Primary B cells from peripheral blood	blood

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