Variant report

Variant	rs4760647
Chromosome Location	chr12:49278643-49278644
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49246388..49252218-chr12:49276087..49280065,7	MCF-7	breast:
2	chr12:49275956..49279461-chr12:49283300..49286531,4	MCF-7	breast:
3	chr12:49253798..49263932-chr12:49272568..49285670,39	MCF-7	breast:
4	chr12:49273861..49275618-chr12:49278332..49280043,2	MCF-7	breast:
5	chr12:49253541..49263542-chr12:49271204..49284916,35	MCF-7	breast:
6	chr12:49244448..49248825-chr12:49273797..49278851,6	MCF-7	breast:
7	chr12:49276917..49280280-chr12:49283219..49286162,3	K562	blood:
8	chr12:49250519..49252141-chr12:49277437..49280181,2	MCF-7	breast:
9	chr12:49265197..49267414-chr12:49276769..49280973,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000174243	Chromatin interaction
ENSG00000172602	Chromatin interaction
ENSG00000199394	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs1051886	0.83[EUR][1000 genomes]
rs1054376	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10747556	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10747557	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10747558	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10783287	0.93[ASN][1000 genomes]
rs10783292	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10783294	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10783295	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10875883	0.93[ASN][1000 genomes]
rs10875886	0.80[AMR][1000 genomes]
rs10875888	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10875893	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10875894	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10875895	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10875896	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10875897	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10875898	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10875900	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10875902	0.83[EUR][1000 genomes]
rs11168769	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11168773	0.92[ASN][1000 genomes]
rs11168779	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11168783	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11168784	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11168785	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11168790	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11168792	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11168794	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11168795	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11168797	0.86[EUR][1000 genomes]
rs11168798	0.80[EUR][1000 genomes]
rs11168800	0.81[EUR][1000 genomes]
rs11168803	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11168812	0.82[EUR][1000 genomes]
rs11608916	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11610459	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11610497	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11614474	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12227240	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12228521	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12229275	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12369505	0.91[ASN][1000 genomes]
rs12423542	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1318692	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1818996	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1830192	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2030900	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2073480	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2131713	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2272311	0.86[EUR][1000 genomes]
rs2272312	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2368701	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2446985	0.90[ASN][1000 genomes]
rs2446986	0.86[ASN][1000 genomes]
rs2446987	0.88[ASN][1000 genomes]
rs2446999	0.96[ASN][1000 genomes]
rs2447000	0.91[ASN][1000 genomes]
rs2447001	0.92[ASN][1000 genomes]
rs2453476	0.87[ASN][1000 genomes]
rs2926806	0.95[ASN][1000 genomes]
rs2934998	0.96[ASN][1000 genomes]
rs3741627	0.83[EUR][1000 genomes]
rs3759146	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3782353	0.83[EUR][1000 genomes]
rs3809147	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3825182	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3958875	0.88[ASN][1000 genomes]
rs4018510	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4237854	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4433614	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4526804	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4760600	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4760661	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4760664	0.83[EUR][1000 genomes]
rs4760665	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4760666	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4760667	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4760668	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58023472	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61941142	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61942166	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61942167	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61942169	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61942207	0.82[EUR][1000 genomes]
rs7134686	0.81[AMR][1000 genomes]
rs7298330	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7489036	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs833476	0.93[ASN][1000 genomes]
rs833478	0.92[ASN][1000 genomes]
rs833479	0.93[ASN][1000 genomes]
rs833483	0.95[ASN][1000 genomes]
rs833484	0.95[ASN][1000 genomes]
rs961320	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9783452	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9783477	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9795742	0.91[AMR][1000 genomes]
rs9796008	0.95[AMR][1000 genomes];0.93[EUR][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	nsv469373	chr12:49256792-49285390	Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
2	nsv558832	chr12:49256792-49285390	Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
3	nsv832404	chr12:49258560-49458555	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4760647	RP11-302B13.1	cis	Whole Blood	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49274000-49278800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:49277400-49279600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr12:49277600-49278800	Weak transcription	Left Ventricle	heart
4	chr12:49277800-49283000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr12:49277800-49284800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr12:49278000-49278800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr12:49278000-49280200	Weak transcription	Gastric	stomach
8	chr12:49278000-49280800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr12:49278000-49284400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr12:49278000-49284400	Weak transcription	Fetal Muscle Leg	muscle
11	chr12:49278200-49279000	Enhancers	A549	lung
12	chr12:49278200-49279600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr12:49278200-49280200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr12:49278200-49280200	Weak transcription	Fetal Intestine Large	intestine
15	chr12:49278200-49280800	Weak transcription	K562	blood
16	chr12:49278200-49281200	Enhancers	HepG2	liver
17	chr12:49278200-49283400	Weak transcription	Brain Germinal Matrix	brain
18	chr12:49278200-49284200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr12:49278200-49284200	Weak transcription	Fetal Intestine Small	intestine
20	chr12:49278200-49284400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:49278400-49280000	Weak transcription	Stomach Mucosa	stomach
22	chr12:49278400-49283800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:49278400-49283800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr12:49278400-49284000	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr12:49278400-49284600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:49278600-49281000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links