Variant report

Variant	rs72840237
Chromosome Location	chr17:45998050-45998051
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:45996385..45998570-chr17:46018249..46020551,2	MCF-7	breast:
2	chr17:45992709..45994396-chr17:45996856..45998957,2	MCF-7	breast:
3	chr17:45972447..45975064-chr17:45996056..45998387,2	MCF-7	breast:
4	chr17:45990771..45994045-chr17:45997430..46001241,5	MCF-7	breast:
5	chr17:45997083..45999024-chr17:46022042..46024143,2	MCF-7	breast:
6	chr17:45995492..45998307-chr17:46023078..46025129,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000264920	Chromatin interaction
ENSG00000234494	Chromatin interaction
ENSG00000263798	Chromatin interaction
ENSG00000108439	Chromatin interaction
ENSG00000167182	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10459927	0.82[ASN][1000 genomes]
rs11079801	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11079803	0.90[ASN][1000 genomes]
rs1108833	0.84[ASN][1000 genomes]
rs1130932	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11652185	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11652827	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11655068	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11655352	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11659126	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11870852	0.84[ASN][1000 genomes]
rs12601827	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12939739	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2228251	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2228253	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2229358	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2318118	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2325747	0.87[ASN][1000 genomes]
rs2325751	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34593510	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36124074	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3764396	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4369725	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4794261	0.84[ASN][1000 genomes]
rs4794286	0.87[ASN][1000 genomes]
rs6503934	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67194241	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7208707	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7211859	0.84[ASN][1000 genomes]
rs8066893	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8071003	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9895863	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9903223	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv518892	chr17:45887951-46029432	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv908575	chr17:45957591-46049533	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
4	nsv1062503	chr17:45977445-46021384	Strong transcription Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs72840237	RP11-6N17.4	cis	Muscle Skeletal	GTEx
rs72840237	RP11-6N17.4	cis	Skin Sun Exposed Lower leg	GTEx
rs72840237	RP11-6N17.4	cis	Thyroid	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45975200-45999400	Weak transcription	Fetal Kidney	kidney
2	chr17:45975200-46000400	Weak transcription	Small Intestine	intestine
3	chr17:45975800-46000600	Weak transcription	Hela-S3	cervix
4	chr17:45979800-46000400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr17:45980200-46001800	Weak transcription	K562	blood
6	chr17:45980200-46002400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr17:45980200-46006400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr17:45982400-46000600	Weak transcription	Stomach Mucosa	stomach
9	chr17:45983000-46001000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr17:45983000-46004000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr17:45983200-46000400	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr17:45983200-46001200	Weak transcription	A549	lung
13	chr17:45983200-46018200	Weak transcription	Fetal Brain Male	brain
14	chr17:45983400-46000600	Weak transcription	NHDF-Ad	bronchial
15	chr17:45984200-46000600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr17:45985600-46000600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr17:45986000-46000400	Weak transcription	Primary hematopoietic stem cells	blood
18	chr17:45987000-46000200	Weak transcription	Aorta	Aorta
19	chr17:45988400-46000400	Weak transcription	Brain Substantia Nigra	brain
20	chr17:45988400-46000600	Weak transcription	HSMM	muscle
21	chr17:45991800-46000400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr17:45991800-46006400	Strong transcription	Fetal Stomach	stomach
23	chr17:45992400-46008400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr17:45992600-46000400	Weak transcription	HSMMtube	muscle
25	chr17:45993400-46000400	Weak transcription	NH-A	brain
26	chr17:45993600-46000600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr17:45993800-46017400	Weak transcription	Psoas Muscle	Psoas
28	chr17:45994000-46000600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr17:45994000-46013200	Weak transcription	Fetal Heart	heart
30	chr17:45994200-46000400	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr17:45994200-46000400	Weak transcription	Left Ventricle	heart
32	chr17:45994200-46006000	Strong transcription	Fetal Muscle Trunk	muscle
33	chr17:45994400-45998400	Weak transcription	GM12878-XiMat	blood
34	chr17:45994400-46000200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr17:45994400-46000400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr17:45994400-46000400	Weak transcription	Gastric	stomach
37	chr17:45994400-46002400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr17:45994400-46006000	Strong transcription	Fetal Muscle Leg	muscle
39	chr17:45994600-45998200	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr17:45994600-45999000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr17:45994600-45999000	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr17:45994600-46000000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr17:45994600-46000000	Weak transcription	Lung	lung
44	chr17:45994600-46000000	Weak transcription	NHLF	lung
45	chr17:45994600-46000200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr17:45994600-46000200	Weak transcription	Colonic Mucosa	Colon
47	chr17:45994600-46000200	Weak transcription	Right Ventricle	heart
48	chr17:45994600-46000400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr17:45994600-46000400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr17:45994600-46000400	Weak transcription	Colon Smooth Muscle	Colon

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