Variant report

Variant	rs7164895
Chromosome Location	chr15:55644411-55644412
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:55644269-55653358	K562	blood:	n/a	n/a
2	RXRA	chr15:55644300-55644470	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:55644113..55647083-chr15:55650261..55652459,2	MCF-7	breast:
2	chr15:55641538..55644525-chr15:55662930..55665274,2	MCF-7	breast:

Variant related genes	Relation type
PIGB	TF binding region
CCPG1	TF binding region
ENSG00000260916	Chromatin interaction
ENSG00000207964	Chromatin interaction

Extended variants
information (count: 125 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs10518810	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1075938	1.00[ASN][1000 genomes]
rs11732	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12101327	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12148255	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12899120	1.00[ASN][1000 genomes]
rs12901464	1.00[ASN][1000 genomes]
rs12902233	1.00[ASN][1000 genomes]
rs12903378	1.00[ASN][1000 genomes]
rs12907135	1.00[ASN][1000 genomes]
rs12909207	1.00[ASN][1000 genomes]
rs12911948	1.00[ASN][1000 genomes]
rs12915831	1.00[ASN][1000 genomes]
rs13329586	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16953240	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976307	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976314	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976351	1.00[ASN][1000 genomes]
rs2414412	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28369251	1.00[ASN][1000 genomes]
rs28378485	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28413009	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28483325	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28636929	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28653717	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3203152	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34473609	1.00[ASN][1000 genomes]
rs34482650	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34659706	1.00[ASN][1000 genomes]
rs34855466	1.00[ASN][1000 genomes]
rs35396030	1.00[ASN][1000 genomes]
rs35720996	1.00[ASN][1000 genomes]
rs35768022	1.00[ASN][1000 genomes]
rs35879962	1.00[ASN][1000 genomes]
rs35928893	1.00[ASN][1000 genomes]
rs36119525	1.00[ASN][1000 genomes]
rs4294762	1.00[ASN][1000 genomes]
rs55706848	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56340826	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56760921	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57094422	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57412310	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57489605	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57648583	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57809907	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58013690	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58053176	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58220352	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58447274	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58507025	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58550265	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58581371	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58697860	1.00[ASN][1000 genomes]
rs58734748	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58743089	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59228226	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59562815	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60003039	1.00[ASN][1000 genomes]
rs60071399	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60439248	1.00[ASN][1000 genomes]
rs60561373	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60755763	1.00[ASN][1000 genomes]
rs60925254	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61069460	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493780	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493781	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71476714	1.00[ASN][1000 genomes]
rs71476716	1.00[ASN][1000 genomes]
rs71476717	1.00[ASN][1000 genomes]
rs71476718	1.00[ASN][1000 genomes]
rs71476719	1.00[ASN][1000 genomes]
rs7161981	1.00[ASN][1000 genomes]
rs7162724	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7164158	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7164984	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168455	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168869	0.81[EUR][1000 genomes]
rs7168882	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169460	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7170157	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7170970	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7173562	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7176013	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7177888	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7181226	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7181805	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7181999	1.00[ASN][1000 genomes]
rs73406912	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73406921	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73406928	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73406986	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73408805	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73408809	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73408827	1.00[ASN][1000 genomes]
rs73421623	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73421633	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73421665	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74015572	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8023354	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8026454	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8027135	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8028482	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8029077	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8029258	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8031507	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8031625	0.91[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs8034029	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8039224	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8040840	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8041044	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8041349	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8041382	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8041885	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8042642	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8043415	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917323	chr15:55290499-56041334	Genic enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv1051046	chr15:55529291-55821973	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1036173	chr15:55547689-55812194	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv542391	chr15:55547689-55812194	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	nsv569523	chr15:55555602-55836704	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	nsv1040917	chr15:55562940-55943942	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv531054	chr15:55571230-55914205	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
9	nsv904243	chr15:55627528-55734158	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv948522	chr15:55639867-56032099	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7164895	CCPG1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55611800-55699400	Weak transcription	Colonic Mucosa	Colon
2	chr15:55612000-55665000	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr15:55612000-55671000	Weak transcription	Right Ventricle	heart
4	chr15:55612000-55671000	Weak transcription	Small Intestine	intestine
5	chr15:55612600-55650200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr15:55612600-55663600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr15:55612600-55675600	Weak transcription	Aorta	Aorta
8	chr15:55612800-55649600	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr15:55612800-55677600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr15:55614800-55649000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr15:55620400-55658000	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr15:55623000-55652600	Weak transcription	Psoas Muscle	Psoas
13	chr15:55623800-55660200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr15:55626000-55649600	Weak transcription	HUVEC	blood vessel
15	chr15:55628600-55647800	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr15:55630000-55695000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr15:55630200-55649000	Weak transcription	Osteobl	bone
18	chr15:55630400-55654600	Weak transcription	Fetal Muscle Trunk	muscle
19	chr15:55630400-55675600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr15:55630600-55648000	Weak transcription	HepG2	liver
21	chr15:55630600-55655800	Weak transcription	Brain Angular Gyrus	brain
22	chr15:55630600-55660200	Weak transcription	Brain Cingulate Gyrus	brain
23	chr15:55630600-55663200	Weak transcription	Fetal Lung	lung
24	chr15:55630600-55667800	Weak transcription	Colon Smooth Muscle	Colon
25	chr15:55630600-55668400	Weak transcription	Brain Substantia Nigra	brain
26	chr15:55630800-55647000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr15:55630800-55652400	Weak transcription	Fetal Muscle Leg	muscle
28	chr15:55630800-55683600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr15:55631000-55667800	Weak transcription	Brain Hippocampus Middle	brain
30	chr15:55631200-55644600	Weak transcription	Fetal Intestine Large	intestine
31	chr15:55631200-55646600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr15:55631200-55663200	Weak transcription	Pancreas	Pancrea
33	chr15:55631200-55674000	Weak transcription	Placenta	Placenta
34	chr15:55631800-55649600	Weak transcription	NH-A	brain
35	chr15:55632000-55646800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr15:55633400-55646400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr15:55633600-55667200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr15:55635800-55675200	Weak transcription	Fetal Brain Male	brain
39	chr15:55636200-55645000	Weak transcription	Fetal Kidney	kidney
40	chr15:55636200-55647000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr15:55636400-55646600	Weak transcription	Primary hematopoietic stem cells	blood
42	chr15:55636600-55649000	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr15:55636600-55657000	Weak transcription	Fetal Brain Female	brain
44	chr15:55636600-55678200	Weak transcription	Fetal Thymus	thymus
45	chr15:55636800-55646000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr15:55636800-55646600	Weak transcription	Adipose Nuclei	Adipose
47	chr15:55636800-55647800	Weak transcription	HSMM	muscle
48	chr15:55636800-55649600	Weak transcription	HMEC	breast
49	chr15:55636800-55651000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr15:55636800-55652000	Weak transcription	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links