Variant report

Variant	rs10817370
Chromosome Location	chr9:115462047-115462048
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:115457008..115459343-chr9:115460680..115462363,2	K562	blood:
2	chr9:115456646..115458575-chr9:115460716..115463371,2	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10759583	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10817374	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10817375	1.00[EUR][1000 genomes]
rs10817377	0.89[EUR][1000 genomes]
rs10817380	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs10817381	1.00[YRI][hapmap]
rs10817388	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs10981483	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981484	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981497	0.81[AMR][1000 genomes]
rs10981501	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs10981524	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs10981527	1.00[YRI][hapmap]
rs11794186	1.00[YRI][hapmap]
rs11794604	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11794827	0.82[MEX][hapmap];1.00[TSI][hapmap]
rs12684608	0.82[MEX][hapmap];1.00[TSI][hapmap]
rs12686677	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1418410	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1517079	1.00[YRI][hapmap]
rs16917411	0.82[MEX][hapmap];1.00[TSI][hapmap]
rs1711739	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1711744	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1711745	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2173195	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2185768	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2798316	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2995805	0.99[ASN][1000 genomes]
rs73534733	0.90[EUR][1000 genomes]
rs786978	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs786979	0.99[ASN][1000 genomes]
rs786981	0.99[ASN][1000 genomes]
rs786983	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:33 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758198	chr9:115240454-116002951	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759710	chr9:115240454-116002951	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv515899	chr9:115359049-115593870	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv34346	chr9:115360505-115581453	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1038999	chr9:115367078-115590950	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	esv2757350	chr9:115371397-115594108	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv471317	chr9:115375153-115558246	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	esv2761275	chr9:115376461-115590962	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1035169	chr9:115378282-115573581	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv1049451	chr9:115378282-115585109	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	nsv1047374	chr9:115378282-115590950	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv1038306	chr9:115379305-115595695	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	nsv540194	chr9:115379305-115595695	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
14	nsv1051909	chr9:115379505-115588377	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
15	nsv540195	chr9:115379505-115588377	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
16	nsv915763	chr9:115379600-115588349	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
17	esv3693040	chr9:115381164-115578065	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
18	nsv515121	chr9:115383227-115585827	Genic enhancers Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
19	nsv1044168	chr9:115383253-115585109	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
20	nsv1048327	chr9:115383253-115589646	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
21	nsv1044381	chr9:115383253-115590950	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
22	nsv442163	chr9:115383255-115590578	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
23	esv35051	chr9:115383332-115573581	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
24	esv34763	chr9:115383332-115581453	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
25	nsv430090	chr9:115383445-115594445	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
26	nsv1041424	chr9:115389428-115590950	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
27	nsv1050186	chr9:115390759-115550453	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
28	nsv1047625	chr9:115390759-115587347	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
29	nsv540196	chr9:115390759-115587347	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
30	nsv615198	chr9:115397206-115589251	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
31	nsv893733	chr9:115397206-115712068	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
32	nsv1051808	chr9:115397891-115590950	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
33	esv34739	chr9:115409445-115581453	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10817370	RAPGEF3	trans	brain	seeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115422200-115479800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:115444000-115479800	Weak transcription	Small Intestine	intestine
3	chr9:115445200-115479200	Weak transcription	Colon Smooth Muscle	Colon
4	chr9:115445600-115476600	Weak transcription	Fetal Brain Male	brain
5	chr9:115446400-115479400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr9:115446600-115462400	Weak transcription	Fetal Heart	heart
7	chr9:115446600-115479400	Weak transcription	Psoas Muscle	Psoas
8	chr9:115447000-115464400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:115447200-115468400	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr9:115448000-115479200	Weak transcription	NHLF	lung
11	chr9:115450400-115466200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr9:115451000-115474400	Weak transcription	Fetal Kidney	kidney
13	chr9:115452000-115475200	Weak transcription	NHDF-Ad	bronchial
14	chr9:115453000-115475800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr9:115453000-115479800	Weak transcription	Gastric	stomach
16	chr9:115453200-115479600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr9:115453400-115473600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr9:115453400-115474400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr9:115453600-115474200	Weak transcription	NHEK	skin
20	chr9:115453800-115465400	Weak transcription	Brain Anterior Caudate	brain
21	chr9:115453800-115474200	Weak transcription	Ovary	ovary
22	chr9:115453800-115478200	Weak transcription	Hela-S3	cervix
23	chr9:115453800-115479200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr9:115453800-115479200	Weak transcription	HUVEC	blood vessel
25	chr9:115453800-115479400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr9:115453800-115479400	Weak transcription	Right Ventricle	heart
27	chr9:115453800-115480000	Weak transcription	Spleen	Spleen
28	chr9:115454200-115479200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr9:115454400-115465800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr9:115454600-115468000	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr9:115454600-115469200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr9:115454600-115479200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr9:115454800-115463400	Weak transcription	Pancreas	Pancrea
34	chr9:115454800-115465600	Weak transcription	Brain Germinal Matrix	brain
35	chr9:115454800-115479200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr9:115454800-115479200	Weak transcription	Rectal Smooth Muscle	rectum
37	chr9:115454800-115479600	Weak transcription	Aorta	Aorta
38	chr9:115455000-115468000	Weak transcription	Brain Hippocampus Middle	brain
39	chr9:115455000-115479800	Weak transcription	Esophagus	oesophagus
40	chr9:115455200-115479400	Weak transcription	Colonic Mucosa	Colon
41	chr9:115455400-115479200	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr9:115455800-115465400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr9:115456000-115465400	Weak transcription	Brain Substantia Nigra	brain
44	chr9:115456000-115479400	Weak transcription	HSMMtube	muscle
45	chr9:115456000-115479600	Weak transcription	Placenta	Placenta
46	chr9:115456400-115477000	Weak transcription	Left Ventricle	heart
47	chr9:115457600-115464000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr9:115457800-115464400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr9:115457800-115468000	Weak transcription	Stomach Mucosa	stomach
50	chr9:115458000-115463200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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