Variant report

Variant	rs7175912
Chromosome Location	chr15:41555249-41555250
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:41555011..41557594-chr15:41575964..41578255,2	K562	blood:
2	chr15:41554916..41558076-chr15:41560482..41563886,4	K562	blood:
3	chr15:41550157..41551774-chr15:41554102..41556216,2	K562	blood:

Variant related genes	Relation type
ENSG00000247556	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10152855	0.83[ASN][1000 genomes]
rs11855102	0.89[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11858115	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11858678	0.92[ASW][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs16971693	0.83[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs16971700	0.86[ASN][1000 genomes]
rs1866400	0.83[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs1965139	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1965140	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1971131	0.83[CHB][hapmap];0.88[CHD][hapmap];0.80[JPT][hapmap]
rs2083239	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2164996	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28409265	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28493237	0.83[ASN][1000 genomes]
rs28495204	0.83[ASN][1000 genomes]
rs28568756	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28615543	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28665387	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28735224	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2899013	0.83[AMR][1000 genomes]
rs2918462	1.00[ASW][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs41442144	0.85[ASN][1000 genomes]
rs4258585	0.83[ASN][1000 genomes]
rs4419033	0.86[AMR][1000 genomes]
rs4445868	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs494490	0.80[GIH][hapmap]
rs55756301	0.81[ASN][1000 genomes]
rs56082289	0.81[ASN][1000 genomes]
rs59389433	0.81[ASN][1000 genomes]
rs59691280	0.81[ASN][1000 genomes]
rs6492991	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6492992	0.81[ASN][1000 genomes]
rs6492993	0.92[ASW][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6492994	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6492997	0.92[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6492998	0.83[TSI][hapmap]
rs690733	0.92[ASW][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs692153	0.80[CHD][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap]
rs7162443	0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7162503	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7166205	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7166905	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7167813	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7170049	0.89[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];0.91[TSI][hapmap]
rs7173086	1.00[ASW][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7178840	0.83[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs7179231	0.83[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs7179969	0.83[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs8026858	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs8032589	0.80[JPT][hapmap]
rs8035252	0.83[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs8036602	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8038834	0.83[CHB][hapmap];0.88[CHD][hapmap];0.80[JPT][hapmap]
rs8039014	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs8039915	0.81[ASN][1000 genomes]
rs8039934	0.83[CHB][hapmap];0.88[CHD][hapmap];0.80[JPT][hapmap]
rs8043253	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs909023	0.83[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs909024	0.83[ASN][1000 genomes]
rs909025	0.88[CHD][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs9972349	0.89[CHB][hapmap];0.85[JPT][hapmap];0.91[YRI][hapmap];0.85[AMR][1000 genomes]
rs9972622	0.84[AMR][1000 genomes]
rs9972623	0.81[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045455	chr15:41536624-41620534	Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs7175912	BUB1B	cis	parietal	SCAN
rs7175912	NDUFAF1	cis	Muscle Skeletal	GTEx
rs7175912	GPR176	cis	parietal	SCAN
rs7175912	CASC5	cis	cerebellum	SCAN
rs7175912	NDUFAF1	cis	lymphoblastoid	seeQTL
rs7175912	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs7175912	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs7175912	NDUFAF1	cis	parietal	SCAN
rs7175912	NDUFAF1	cis	Thyroid	GTEx
rs7175912	NDUFAF1	cis	cerebellum	SCAN
rs7175912	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs7175912	NUSAP1	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41524200-41555800	Weak transcription	Aorta	Aorta
2	chr15:41524200-41563800	Weak transcription	Small Intestine	intestine
3	chr15:41524200-41575800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:41524400-41555800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr15:41524800-41563800	Weak transcription	Esophagus	oesophagus
6	chr15:41525200-41556400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr15:41525200-41575400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr15:41525400-41556200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr15:41525400-41556800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr15:41525800-41575200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr15:41534200-41556400	Weak transcription	Spleen	Spleen
12	chr15:41536600-41573600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr15:41537400-41570800	Weak transcription	Ovary	ovary
14	chr15:41537600-41562800	Weak transcription	Lung	lung
15	chr15:41539400-41555800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr15:41542800-41572000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr15:41543000-41575200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr15:41545000-41571400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr15:41549200-41555400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr15:41549200-41575200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr15:41549800-41556200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr15:41550400-41571400	Weak transcription	Right Ventricle	heart
23	chr15:41550400-41575600	Weak transcription	Fetal Brain Male	brain
24	chr15:41550600-41564200	Weak transcription	NHDF-Ad	bronchial
25	chr15:41550800-41556000	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr15:41551800-41568600	Weak transcription	Fetal Lung	lung
27	chr15:41551800-41570600	Weak transcription	HMEC	breast
28	chr15:41552200-41555800	Weak transcription	Fetal Heart	heart
29	chr15:41552400-41555400	Weak transcription	Pancreas	Pancrea
30	chr15:41552400-41555800	Weak transcription	Psoas Muscle	Psoas
31	chr15:41552400-41574600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr15:41552600-41575200	Weak transcription	GM12878-XiMat	blood
33	chr15:41552800-41575800	Weak transcription	Primary hematopoietic stem cells	blood
34	chr15:41553000-41560000	Strong transcription	Fetal Intestine Small	intestine
35	chr15:41553600-41569200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr15:41554200-41555800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr15:41554200-41557200	Strong transcription	Fetal Brain Female	brain
38	chr15:41554400-41555400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr15:41554400-41555400	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr15:41554400-41555800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr15:41554400-41557200	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr15:41554400-41557600	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr15:41554400-41559600	Strong transcription	Fetal Muscle Trunk	muscle
44	chr15:41554600-41555400	Strong transcription	HSMM	muscle
45	chr15:41554600-41555600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr15:41554600-41555600	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr15:41554600-41555600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr15:41554600-41555600	Strong transcription	Left Ventricle	heart
49	chr15:41554600-41555600	Strong transcription	NHEK	skin
50	chr15:41554600-41555800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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