Variant report

Variant	rs17658724
Chromosome Location	chr9:3259659-3259660
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:3254757..3256417-chr9:3258277..3260050,2	K562	blood:

Extended variants
information (count: 107 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10429463	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1147822	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11998979	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12004313	0.91[EUR][1000 genomes]
rs12004744	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1443205	0.81[EUR][1000 genomes]
rs16916423	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17658838	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17715051	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17715160	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17715317	0.94[EUR][1000 genomes]
rs17715329	0.88[EUR][1000 genomes]
rs2304928	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2920363	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2920369	0.90[EUR][1000 genomes]
rs2920370	0.91[EUR][1000 genomes]
rs2920375	0.81[EUR][1000 genomes]
rs2920381	0.83[EUR][1000 genomes]
rs2920383	0.89[EUR][1000 genomes]
rs2986686	0.91[EUR][1000 genomes]
rs2986687	0.86[EUR][1000 genomes]
rs2986693	0.82[EUR][1000 genomes]
rs2986695	0.89[EUR][1000 genomes]
rs2986696	0.89[EUR][1000 genomes]
rs2986697	0.89[EUR][1000 genomes]
rs2986698	0.89[EUR][1000 genomes]
rs2986700	0.89[EUR][1000 genomes]
rs2986701	0.87[EUR][1000 genomes]
rs2986702	0.86[EUR][1000 genomes]
rs2986703	0.85[EUR][1000 genomes]
rs2991297	0.81[EUR][1000 genomes]
rs2991298	0.81[EUR][1000 genomes]
rs2991300	0.82[EUR][1000 genomes]
rs2991301	0.87[EUR][1000 genomes]
rs2991305	0.89[EUR][1000 genomes]
rs2991306	0.83[EUR][1000 genomes]
rs2991307	0.88[EUR][1000 genomes]
rs2991308	0.86[EUR][1000 genomes]
rs2991310	0.86[EUR][1000 genomes]
rs2991311	0.86[EUR][1000 genomes]
rs2991318	0.83[EUR][1000 genomes]
rs3012680	0.86[ASN][1000 genomes]
rs3012686	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3012688	0.85[EUR][1000 genomes]
rs3012693	0.90[EUR][1000 genomes]
rs3012695	0.91[EUR][1000 genomes]
rs3012696	0.91[EUR][1000 genomes]
rs3012700	0.90[EUR][1000 genomes]
rs3012701	0.87[EUR][1000 genomes]
rs3012705	0.82[EUR][1000 genomes]
rs3012707	0.85[EUR][1000 genomes]
rs3012710	0.87[EUR][1000 genomes]
rs4008965	0.87[EUR][1000 genomes]
rs41312820	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs490961	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs494348	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs506149	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs515913	0.81[ASN][1000 genomes]
rs527697	0.85[EUR][1000 genomes]
rs535305	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs540859	0.87[EUR][1000 genomes]
rs57295144	0.88[EUR][1000 genomes]
rs576347	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58010475	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59378342	0.88[EUR][1000 genomes]
rs594370	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs612198	0.91[EUR][1000 genomes]
rs617047	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs617992	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs619401	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs625941	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs633893	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs636548	0.83[EUR][1000 genomes]
rs645583	0.81[EUR][1000 genomes]
rs646529	0.91[ASN][1000 genomes]
rs649990	0.83[EUR][1000 genomes]
rs656686	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs658123	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7025201	0.86[EUR][1000 genomes]
rs7025328	0.90[EUR][1000 genomes]
rs7035429	0.83[EUR][1000 genomes]
rs7044448	0.93[EUR][1000 genomes]
rs72697092	0.81[ASN][1000 genomes]
rs72699004	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72699014	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72699023	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72699031	0.81[ASN][1000 genomes]
rs72699033	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72699037	0.89[EUR][1000 genomes]
rs72699039	0.93[EUR][1000 genomes]
rs72699050	0.85[EUR][1000 genomes]
rs72699051	0.89[EUR][1000 genomes]
rs7850999	0.90[EUR][1000 genomes]
rs7855172	0.89[AFR][1000 genomes]
rs7859468	0.87[EUR][1000 genomes]
rs7860020	0.87[EUR][1000 genomes]
rs7866129	0.87[EUR][1000 genomes]
rs7868041	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv1028668	chr9:3139007-3262791	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv539939	chr9:3139007-3262791	Bivalent Enhancer Strong transcription Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	nsv1032529	chr9:3254763-3319778	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv539941	chr9:3254763-3319778	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3220400-3287400	Weak transcription	Psoas Muscle	Psoas
2	chr9:3222200-3269400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr9:3223200-3277000	Weak transcription	HSMMtube	muscle
4	chr9:3223400-3270200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr9:3223600-3264400	Weak transcription	Fetal Intestine Small	intestine
6	chr9:3223600-3271600	Weak transcription	Lung	lung
7	chr9:3223600-3284800	Weak transcription	Spleen	Spleen
8	chr9:3224000-3275800	Weak transcription	Gastric	stomach
9	chr9:3225200-3262800	Weak transcription	Esophagus	oesophagus
10	chr9:3226600-3289600	Weak transcription	Colon Smooth Muscle	Colon
11	chr9:3233600-3292600	Weak transcription	Pancreas	Pancrea
12	chr9:3234800-3294400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr9:3235800-3269800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr9:3236200-3271600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr9:3236800-3266600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr9:3238000-3276800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr9:3238600-3263800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr9:3241400-3278000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr9:3241600-3276800	Weak transcription	Placenta	Placenta
20	chr9:3241800-3271200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr9:3242000-3262400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr9:3242000-3278000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr9:3242200-3261400	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr9:3242200-3287800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr9:3242800-3261600	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr9:3243800-3262600	Weak transcription	Dnd41	blood
27	chr9:3243800-3279200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr9:3244000-3262600	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr9:3244000-3268200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr9:3244200-3338400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr9:3244600-3262600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr9:3245000-3265800	Weak transcription	Stomach Mucosa	stomach
33	chr9:3245000-3275000	Weak transcription	HSMM	muscle
34	chr9:3245600-3277200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr9:3246200-3262600	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr9:3246800-3287000	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr9:3250200-3276400	Weak transcription	HepG2	liver
38	chr9:3251000-3262600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr9:3251600-3292600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr9:3251800-3262800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr9:3252800-3278600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr9:3254200-3285600	Weak transcription	Fetal Heart	heart
43	chr9:3254800-3272000	Weak transcription	NH-A	brain
44	chr9:3255000-3293000	Weak transcription	Small Intestine	intestine
45	chr9:3255800-3264800	Weak transcription	Brain Angular Gyrus	brain
46	chr9:3255800-3292800	Weak transcription	Fetal Muscle Leg	muscle
47	chr9:3256400-3263000	Weak transcription	Fetal Stomach	stomach
48	chr9:3256800-3262600	Weak transcription	Fetal Muscle Trunk	muscle
49	chr9:3256800-3293400	Weak transcription	Right Ventricle	heart
50	chr9:3257000-3261200	Weak transcription	Primary hematopoietic stem cells	blood

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