Variant report

Variant	rs4768740
Chromosome Location	chr12:47055313-47055314
allele	C/T
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:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:46972689..46974788-chr12:47053934..47056734,2	MCF-7	breast:
2	chr12:46747621..46748674-chr12:47054938..47055840,3	MCF-7	breast:
3	chr12:47054064..47055917-chr12:47057458..47059164,2	K562	blood:
4	chr12:46756339..46758839-chr12:47053863..47055501,2	MCF-7	breast:
5	chr12:46775880..46778772-chr12:47053263..47055840,3	MCF-7	breast:
6	chr12:46759450..46767729-chr12:47050364..47062392,28	MCF-7	breast:
7	chr12:46886016..46887722-chr12:47054283..47056459,2	MCF-7	breast:
8	chr12:46383988..46386138-chr12:47055082..47056612,2	MCF-7	breast:
9	chr12:46760654..46769647-chr12:47051646..47061944,32	MCF-7	breast:
10	chr12:46757823..46760512-chr12:47053505..47055776,2	K562	blood:
11	chr12:46775360..46780494-chr12:47054865..47060216,9	MCF-7	breast:
12	chr12:46887516..46889882-chr12:47054053..47056770,2	MCF-7	breast:
13	chr12:47053397..47056382-chr12:47060303..47062102,2	MCF-7	breast:
14	chr12:46762091..46766718-chr12:47051293..47055848,8	K562	blood:
15	chr12:46764217..46768302-chr12:47052891..47055832,5	K562	blood:
16	chr12:46776215..46777851-chr12:47053337..47055678,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000134294	Chromatin interaction
ENSG00000139218	Chromatin interaction
ENSG00000257261	Chromatin interaction
ENSG00000258096	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11183519	0.85[JPT][hapmap];0.82[AMR][1000 genomes]
rs11183551	0.86[AMR][1000 genomes]
rs11183610	0.90[MEX][hapmap]
rs12301825	0.83[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.81[MEX][hapmap];0.81[AMR][1000 genomes]
rs12311952	0.84[JPT][hapmap];0.84[AMR][1000 genomes]
rs12318944	0.82[AMR][1000 genomes]
rs12579010	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12579419	0.96[AMR][1000 genomes]
rs12579984	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12580176	0.94[AMR][1000 genomes]
rs12581743	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1266371	0.84[AMR][1000 genomes]
rs17097079	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs17097091	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs17097141	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17097246	0.90[MEX][hapmap]
rs180431	0.90[MEX][hapmap]
rs1946174	0.85[AMR][1000 genomes]
rs1986154	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2160892	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2287470	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs235621	0.91[MEX][hapmap]
rs235622	0.86[MEX][hapmap]
rs235626	0.86[MEX][hapmap]
rs2408616	1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2897979	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4351902	0.96[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4768124	0.83[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes]
rs4768126	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4768738	0.93[ASN][1000 genomes]
rs4768741	0.86[MEX][hapmap]
rs4768746	0.83[ASN][1000 genomes]
rs4768747	0.91[ASN][1000 genomes]
rs4768749	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs57616927	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58806862	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs59408501	0.82[AMR][1000 genomes]
rs7132144	0.80[AMR][1000 genomes]
rs7133051	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7310614	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7311414	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7315740	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73282105	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73282110	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7487359	0.83[JPT][hapmap];0.82[AMR][1000 genomes]
rs7959179	0.89[ASN][1000 genomes]
rs7971812	0.86[ASN][1000 genomes]
rs7976531	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7976785	0.80[AMR][1000 genomes]
rs7979449	0.86[ASN][1000 genomes]
rs977069	0.89[LWK][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.83[YRI][hapmap]

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	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
3	esv3416674	chr12:46988689-47178369	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv558783	chr12:46996632-47144856	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv1844378	chr12:47028797-47072016	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv1845143	chr12:47051076-47431496	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47046400-47069800	Weak transcription	Pancreas	Pancrea
2	chr12:47046800-47057000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:47050800-47056000	Enhancers	NHLF	lung
4	chr12:47051000-47056200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr12:47051400-47055600	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr12:47051400-47055800	Enhancers	Fetal Heart	heart
7	chr12:47051400-47055800	Enhancers	HSMM	muscle
8	chr12:47051400-47056200	Enhancers	HUVEC	blood vessel
9	chr12:47051400-47059800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr12:47051600-47055600	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr12:47051800-47055400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr12:47051800-47056000	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr12:47051800-47056000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr12:47052200-47055600	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr12:47052400-47055600	Enhancers	Primary T cells from cord blood	blood
16	chr12:47052600-47055400	Enhancers	Fetal Stomach	stomach
17	chr12:47052600-47056000	Enhancers	Primary hematopoietic stem cells	blood
18	chr12:47052800-47055400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr12:47052800-47055400	Enhancers	Fetal Muscle Leg	muscle
20	chr12:47053000-47055800	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr12:47053200-47055400	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr12:47053200-47055600	Enhancers	Primary B cells from peripheral blood	blood
23	chr12:47053200-47055800	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr12:47053400-47055400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr12:47053400-47055400	Enhancers	Adipose Nuclei	Adipose
26	chr12:47053400-47055400	Enhancers	Rectal Smooth Muscle	rectum
27	chr12:47053400-47055400	Enhancers	NHDF-Ad	bronchial
28	chr12:47053400-47055600	Enhancers	Fetal Lung	lung
29	chr12:47053400-47055800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr12:47053400-47058200	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr12:47053400-47058600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr12:47053400-47062400	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr12:47053600-47055600	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr12:47053600-47055600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr12:47053600-47055800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr12:47053600-47056000	Enhancers	NH-A	brain
37	chr12:47053600-47056200	Enhancers	HMEC	breast
38	chr12:47053800-47055400	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr12:47053800-47055600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr12:47053800-47058800	Enhancers	Hela-S3	cervix
41	chr12:47054000-47055800	Enhancers	Dnd41	blood
42	chr12:47054000-47068400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr12:47054000-47071400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:47054200-47055400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr12:47054200-47055600	Enhancers	Fetal Kidney	kidney
46	chr12:47054200-47055600	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr12:47054400-47055400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr12:47054400-47055400	Enhancers	Thymus	Thymus
49	chr12:47054400-47055800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr12:47054400-47056000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links