Variant report

Variant	rs71395066
Chromosome Location	chr15:72456429-72456430
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	chr15:72456159-72456429	H1-neurons	neurons:	n/a	n/a
2	NR3C1	chr15:72456222-72456587	A549	lung:	n/a	n/a
3	REST	chr15:72455666-72456751	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr15:72455846-72456605	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:72454000..72456435-chr15:72458895..72460767,2	MCF-7	breast:
2	chr15:72454028..72456200-chr15:72456374..72458643,3	MCF-7	breast:

Variant related genes	Relation type
GRAMD2	TF binding region
ENSG00000175318	Chromatin interaction

Extended variants
information (count: 135 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:129)

rs_ID	r²[population]
rs10518987	1.00[ASN][1000 genomes]
rs10732234	1.00[AMR][1000 genomes]
rs11632505	0.94[ASN][1000 genomes]
rs12324744	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12899442	0.84[ASN][1000 genomes]
rs12902160	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12904667	0.84[ASN][1000 genomes]
rs12905794	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12905947	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12906356	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12906612	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12907087	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12907377	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12907707	0.94[ASN][1000 genomes]
rs12908241	0.94[ASN][1000 genomes]
rs12908863	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12909590	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12910475	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12910620	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12911278	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12911285	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12914208	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12914269	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12914312	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12915008	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12916039	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12916226	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12916298	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12916789	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12917402	0.84[ASN][1000 genomes]
rs12917442	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1426169	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2277543	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2288257	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2912203	0.94[ASN][1000 genomes]
rs2912204	0.94[ASN][1000 genomes]
rs2912215	0.94[ASN][1000 genomes]
rs2912222	0.94[ASN][1000 genomes]
rs2912224	0.94[ASN][1000 genomes]
rs2912225	0.94[ASN][1000 genomes]
rs2957751	0.88[ASN][1000 genomes]
rs2957752	0.94[ASN][1000 genomes]
rs2959916	0.94[ASN][1000 genomes]
rs2959917	0.94[ASN][1000 genomes]
rs2959918	0.94[ASN][1000 genomes]
rs2959919	0.94[ASN][1000 genomes]
rs2959923	0.94[ASN][1000 genomes]
rs2959924	0.94[ASN][1000 genomes]
rs2959927	0.94[ASN][1000 genomes]
rs2959929	0.94[ASN][1000 genomes]
rs2959931	0.94[ASN][1000 genomes]
rs2959933	0.94[ASN][1000 genomes]
rs2959935	0.94[ASN][1000 genomes]
rs2959940	0.84[ASN][1000 genomes]
rs34023258	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34115124	0.94[ASN][1000 genomes]
rs34211376	0.94[ASN][1000 genomes]
rs34294127	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34346715	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34362323	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs34382909	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34481625	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs34505994	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34511502	0.94[ASN][1000 genomes]
rs34538801	0.94[ASN][1000 genomes]
rs34638996	1.00[AMR][1000 genomes]
rs34658339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34677662	0.94[ASN][1000 genomes]
rs34694253	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34705283	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs34789424	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34815962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35061524	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs35071085	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35104697	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35136885	1.00[AMR][1000 genomes]
rs35144689	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs35202897	0.94[ASN][1000 genomes]
rs35259670	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs35285520	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35288005	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs35362359	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs35378070	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35408293	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs35457238	0.94[ASN][1000 genomes]
rs35491098	0.81[ASN][1000 genomes]
rs35554838	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs35694406	1.00[ASN][1000 genomes]
rs35836103	1.00[AMR][1000 genomes]
rs36110969	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3743227	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3743228	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3743229	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3759817	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3759819	0.81[ASN][1000 genomes]
rs3759821	0.81[ASN][1000 genomes]
rs3759901	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3825949	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4776592	0.84[ASN][1000 genomes]
rs4776593	0.84[ASN][1000 genomes]
rs4777501	0.84[ASN][1000 genomes]
rs55935015	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs57420281	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57692836	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58352854	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs66608810	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs67195650	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs71395049	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs71395050	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs71395056	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs71395057	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs71395058	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs71395061	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs71395068	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs71395070	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs71395074	0.94[ASN][1000 genomes]
rs71397231	0.94[ASN][1000 genomes]
rs71397232	0.94[ASN][1000 genomes]
rs71397233	0.94[ASN][1000 genomes]
rs71411063	0.94[ASN][1000 genomes]
rs7169150	1.00[ASN][1000 genomes]
rs7174264	1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73438446	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8192359	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8192387	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8192397	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs890312	1.00[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9806184	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9806204	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042740	chr15:72128799-72482239	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv542426	chr15:72128799-72482239	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv431395	chr15:72266174-72701777	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
4	nsv833051	chr15:72315471-72508429	Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv530817	chr15:72350885-72773374	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
6	esv3430860	chr15:72373723-72849907	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72448400-72458800	Weak transcription	Spleen	Spleen
2	chr15:72448400-72460800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr15:72448600-72458600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr15:72448600-72460800	Weak transcription	Colon Smooth Muscle	Colon
5	chr15:72448600-72460800	Weak transcription	Right Atrium	heart
6	chr15:72448800-72459800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr15:72448800-72460400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr15:72448800-72462400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr15:72449000-72459200	Weak transcription	HMEC	breast
10	chr15:72449000-72459800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr15:72449200-72460400	Weak transcription	Fetal Kidney	kidney
12	chr15:72449200-72462200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr15:72453000-72459800	Strong transcription	Fetal Intestine Small	intestine
14	chr15:72453000-72460000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr15:72453200-72456800	Genic enhancers	Placenta	Placenta
16	chr15:72454400-72471400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr15:72454600-72460000	Weak transcription	Fetal Intestine Large	intestine
18	chr15:72454600-72460600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr15:72455200-72458400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr15:72455200-72458800	Weak transcription	Fetal Lung	lung
21	chr15:72455200-72459400	Weak transcription	Fetal Stomach	stomach
22	chr15:72455200-72460000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr15:72455200-72460000	Weak transcription	Lung	lung
24	chr15:72455200-72460400	Weak transcription	Fetal Muscle Leg	muscle
25	chr15:72455600-72456600	Enhancers	Fetal Brain Male	brain
26	chr15:72455800-72456600	Enhancers	Brain Hippocampus Middle	brain
27	chr15:72456000-72456600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr15:72456000-72456600	Active TSS	Hela-S3	cervix
29	chr15:72456000-72456800	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr15:72456000-72456800	Enhancers	Fetal Brain Female	brain
31	chr15:72456200-72456600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr15:72456200-72456800	Enhancers	Brain Anterior Caudate	brain
33	chr15:72456400-72456600	Enhancers	Brain Angular Gyrus	brain
34	chr15:72456400-72456600	Enhancers	Brain Cingulate Gyrus	brain
35	chr15:72456400-72456600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr15:72456400-72457000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr15:72456400-72460400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links