Variant report

Variant	rs7164298
Chromosome Location	chr15:57583301-57583302
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:57575333..57577796-chr15:57582092..57585036,2	K562	blood:
2	chr15:57523231..57525138-chr15:57581607..57583669,2	K562	blood:
3	chr15:57582041..57585604-chr15:57586782..57591985,5	K562	blood:
4	chr15:57582135..57584182-chr15:57589221..57591985,2	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10467927	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs10467928	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs10467929	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs11071308	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap]
rs11853810	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11856210	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13379847	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs16977243	0.95[GIH][hapmap]
rs16977270	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs16977278	1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap];0.82[ASN][1000 genomes]
rs16977306	0.82[CEU][hapmap]
rs16977374	0.82[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.91[TSI][hapmap];0.99[ASN][1000 genomes]
rs2169467	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs2414493	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs2593211	0.82[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap]
rs2593249	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2593252	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs2615226	0.92[ASN][1000 genomes]
rs2615227	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2703593	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs2703595	0.81[TSI][hapmap]
rs2703614	0.83[CHB][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.83[TSI][hapmap]
rs2733310	0.82[CEU][hapmap]
rs2733323	0.88[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap]
rs2733333	0.83[CHB][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap]
rs2733334	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28445470	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28653088	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3803453	0.89[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4774915	0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4774916	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4774921	0.83[ASN][1000 genomes]
rs55742030	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6493907	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7164914	0.86[ASN][1000 genomes]
rs7173477	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7173748	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7179311	0.87[CEU][hapmap]
rs7180558	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.95[ASN][1000 genomes]
rs7181399	0.82[CEU][hapmap]
rs720290	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs8024901	0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.97[ASN][1000 genomes]
rs8026702	0.82[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.84[ASN][1000 genomes]
rs8034502	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8034744	0.82[CEU][hapmap];0.89[TSI][hapmap]
rs8034843	0.88[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8035916	0.89[JPT][hapmap]
rs8037956	0.80[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[YRI][hapmap];0.97[ASN][1000 genomes]
rs8039176	1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.97[ASN][1000 genomes]
rs9672676	0.88[CEU][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap]
rs9806170	0.83[CHB][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap]
rs9806199	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs997683	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv833021	chr15:57495413-57751366	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv526342	chr15:57565859-57597280	Strong transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7164298	TCF12	Cis_1M	lymphoblastoid	RTeQTL
rs7164298	AQP9	cis	cerebellum	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57522800-57585000	Strong transcription	Fetal Thymus	thymus
2	chr15:57537800-57598200	Weak transcription	Colonic Mucosa	Colon
3	chr15:57552200-57588600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr15:57553200-57585000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr15:57557000-57584600	Weak transcription	Colon Smooth Muscle	Colon
6	chr15:57557600-57588600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:57562600-57584200	Strong transcription	Fetal Muscle Trunk	muscle
8	chr15:57562600-57584600	Strong transcription	Fetal Muscle Leg	muscle
9	chr15:57564000-57583600	Strong transcription	Dnd41	blood
10	chr15:57564800-57584600	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr15:57565000-57583400	Strong transcription	Thymus	Thymus
12	chr15:57565600-57584600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr15:57566000-57584400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr15:57566000-57591600	Weak transcription	Esophagus	oesophagus
15	chr15:57568000-57588400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr15:57568000-57590600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr15:57568200-57591600	Weak transcription	Psoas Muscle	Psoas
18	chr15:57568600-57583800	Strong transcription	Fetal Intestine Large	intestine
19	chr15:57571400-57583600	Strong transcription	Liver	Liver
20	chr15:57571400-57584800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr15:57572200-57584200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr15:57573800-57589000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr15:57574200-57583400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr15:57575000-57589200	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr15:57577000-57583400	Enhancers	Primary B cells from peripheral blood	blood
26	chr15:57578200-57583400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr15:57578200-57589200	Weak transcription	Pancreas	Pancrea
28	chr15:57578600-57591600	Weak transcription	Spleen	Spleen
29	chr15:57578600-57598200	Weak transcription	Right Ventricle	heart
30	chr15:57578800-57588400	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr15:57578800-57592800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr15:57579200-57585000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr15:57579200-57585600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr15:57579200-57588600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr15:57579200-57589600	Weak transcription	Rectal Smooth Muscle	rectum
36	chr15:57579200-57592800	Weak transcription	Small Intestine	intestine
37	chr15:57579600-57589200	Weak transcription	Brain Substantia Nigra	brain
38	chr15:57579600-57598200	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr15:57579800-57588800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr15:57579800-57589200	Weak transcription	Brain Anterior Caudate	brain
41	chr15:57579800-57590400	Weak transcription	Brain Angular Gyrus	brain
42	chr15:57579800-57595000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr15:57580000-57584600	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr15:57580000-57588000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr15:57580000-57598400	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr15:57580000-57598400	Weak transcription	Fetal Brain Male	brain
47	chr15:57580000-57598400	Weak transcription	NHEK	skin
48	chr15:57580200-57588600	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr15:57580200-57588600	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr15:57580200-57589000	Weak transcription	Fetal Brain Female	brain

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