Variant report

Variant	rs10972200
Chromosome Location	chr9:3479416-3479417
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:3479015..3481934-chr9:3484671..3486572,2	K562	blood:
2	chr9:3478923..3481537-chr9:3524337..3526099,2	K562	blood:
3	chr9:3478739..3481374-chr9:3498869..3500820,2	MCF-7	breast:
4	chr9:3477335..3480982-chr9:3525320..3527937,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000080298	Chromatin interaction
ENSG00000232104	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10113926	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10114162	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10114838	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10115578	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10117292	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10119475	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10119982	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10121096	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10123122	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10123592	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10124613	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10758273	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10758286	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10814148	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10972184	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12238307	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12340274	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12353393	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1342542	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7026025	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7027858	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7037463	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7857554	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7861625	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs881167	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	nsv892090	chr9:3391364-3496660	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1019324	chr9:3436845-3502815	ZNF genes & repeats Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv1022795	chr9:3436845-3744623	Enhancers Flanking Active TSS Weak transcription Strong transcription 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	32 gene(s)	inside rSNPs	diseases
12	nsv892091	chr9:3459635-3508284	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv539944	chr9:3476471-3535344	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3455000-3483000	Weak transcription	Fetal Thymus	thymus
2	chr9:3468000-3480800	Weak transcription	NHDF-Ad	bronchial
3	chr9:3468200-3482200	Weak transcription	A549	lung
4	chr9:3468600-3480200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr9:3468600-3483800	Weak transcription	Brain Hippocampus Middle	brain
6	chr9:3468600-3484800	Weak transcription	Ovary	ovary
7	chr9:3468800-3496600	Weak transcription	HSMMtube	muscle
8	chr9:3469400-3495600	Weak transcription	Fetal Kidney	kidney
9	chr9:3471000-3480600	Enhancers	HUVEC	blood vessel
10	chr9:3472000-3480400	Weak transcription	Fetal Heart	heart
11	chr9:3473600-3496600	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr9:3473800-3482200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr9:3474000-3493600	Weak transcription	Fetal Stomach	stomach
14	chr9:3474400-3490800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr9:3474400-3524400	Weak transcription	Thymus	Thymus
16	chr9:3474600-3486000	Weak transcription	Small Intestine	intestine
17	chr9:3475000-3492600	Weak transcription	Lung	lung
18	chr9:3475600-3480200	Weak transcription	Pancreas	Pancrea
19	chr9:3475800-3480000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr9:3475800-3481000	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr9:3475800-3483400	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr9:3475800-3485600	Weak transcription	Spleen	Spleen
23	chr9:3476400-3480800	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr9:3477200-3480800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr9:3477200-3480800	Enhancers	Primary B cells from cord blood	blood
26	chr9:3477200-3481000	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr9:3477400-3485400	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr9:3477600-3484400	Weak transcription	Fetal Muscle Trunk	muscle
29	chr9:3477600-3487000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr9:3477600-3495600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr9:3477800-3480000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr9:3477800-3480200	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr9:3477800-3480600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr9:3477800-3481200	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr9:3477800-3483400	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr9:3477800-3483600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr9:3477800-3486200	Weak transcription	Duodenum Mucosa	Duodenum
38	chr9:3478000-3480600	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr9:3478000-3486000	Weak transcription	Liver	Liver
40	chr9:3478200-3480800	Enhancers	Primary B cells from peripheral blood	blood
41	chr9:3478200-3481200	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr9:3478200-3484400	Weak transcription	Brain Anterior Caudate	brain
43	chr9:3478200-3485200	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr9:3478200-3488000	Weak transcription	Fetal Intestine Large	intestine
45	chr9:3478400-3479800	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr9:3478400-3479800	Enhancers	NHEK	skin
47	chr9:3478400-3480200	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr9:3478400-3481000	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr9:3478600-3479800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr9:3478600-3479800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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