Variant report

Variant	rs6856569
Chromosome Location	chr4:152130499-152130500
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:152124247..152127110-chr4:152129155..152131001,2	MCF-7	breast:
2	chr4:152118284..152119881-chr4:152128835..152131528,2	K562	blood:

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10000557	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10001039	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10005907	0.83[ASN][1000 genomes]
rs10016998	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10017154	0.88[EUR][1000 genomes]
rs10030785	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10213332	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10776521	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10776523	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10857254	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10857255	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10857256	0.83[ASN][1000 genomes]
rs11099787	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11099788	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11099790	0.84[EUR][1000 genomes]
rs11099791	0.86[ASN][1000 genomes]
rs11099794	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11099795	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11726180	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11729981	0.93[ASN][1000 genomes]
rs11730087	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11734586	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11943477	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12500168	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12500223	0.93[ASN][1000 genomes]
rs13123932	0.83[ASN][1000 genomes]
rs13148755	0.81[EUR][1000 genomes]
rs13149045	0.93[ASN][1000 genomes]
rs1316364	0.93[ASN][1000 genomes]
rs1320006	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1320007	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1320192	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1878796	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2407406	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2407411	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2407414	0.81[AFR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2407415	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2407424	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2407425	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2407426	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2407427	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2407428	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2407429	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2407430	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2407440	0.81[ASN][1000 genomes]
rs2897657	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2897660	0.81[ASN][1000 genomes]
rs4434229	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4616734	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4696235	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4696237	0.93[ASN][1000 genomes]
rs6535767	0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6535775	0.88[ASN][1000 genomes]
rs6535776	0.93[ASN][1000 genomes]
rs6812695	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6815608	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6823953	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6825613	0.81[ASN][1000 genomes]
rs6825952	0.81[ASN][1000 genomes]
rs6828937	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6829963	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6837905	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6838301	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6838845	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6847669	0.93[ASN][1000 genomes]
rs7666751	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7668154	0.81[ASN][1000 genomes]
rs7681030	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7687117	0.93[ASN][1000 genomes]
rs7690329	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7695005	0.93[ASN][1000 genomes]
rs938990	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034948	chr4:151590115-152202687	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv537302	chr4:151590115-152202687	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv530159	chr4:151624865-152203910	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv948719	chr4:151693149-152161625	Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv880262	chr4:151712054-152519899	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv881526	chr4:151968295-152489087	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv1016220	chr4:151997139-152164126	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv537306	chr4:151997139-152164126	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
9	nsv870229	chr4:152114410-152161072	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152097200-152136600	Weak transcription	Colonic Mucosa	Colon
2	chr4:152098400-152147200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr4:152117600-152148800	Weak transcription	Esophagus	oesophagus
4	chr4:152118800-152146600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:152119000-152139400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:152119400-152139400	Weak transcription	NHEK	skin
7	chr4:152120800-152153800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr4:152121000-152136400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:152121000-152138000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:152121200-152133800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr4:152124400-152136400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr4:152124400-152139600	Weak transcription	Osteobl	bone
13	chr4:152124400-152147000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr4:152124600-152136200	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr4:152124600-152139400	Weak transcription	HSMM	muscle
16	chr4:152124600-152139600	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr4:152124600-152139800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr4:152124600-152146800	Weak transcription	HSMMtube	muscle
19	chr4:152124800-152136400	Weak transcription	NH-A	brain
20	chr4:152124800-152140000	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr4:152126400-152147200	Weak transcription	Fetal Muscle Trunk	muscle
22	chr4:152126800-152147000	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr4:152127200-152136400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr4:152128000-152140600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr4:152128000-152141600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr4:152128400-152138000	Weak transcription	Fetal Stomach	stomach
27	chr4:152128400-152139600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr4:152128400-152146600	Weak transcription	HMEC	breast
29	chr4:152128400-152146800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr4:152128600-152147200	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr4:152129000-152130600	Weak transcription	Small Intestine	intestine
32	chr4:152129000-152131000	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr4:152129000-152136200	Weak transcription	Left Ventricle	heart
34	chr4:152129000-152139200	Weak transcription	NHDF-Ad	bronchial
35	chr4:152129000-152139600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr4:152129000-152146800	Weak transcription	Brain Angular Gyrus	brain
37	chr4:152129000-152148800	Weak transcription	Fetal Intestine Large	intestine
38	chr4:152129000-152168000	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr4:152129200-152130600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr4:152129200-152133600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr4:152129200-152136400	Weak transcription	Brain Hippocampus Middle	brain
42	chr4:152129200-152136600	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr4:152129200-152136800	Weak transcription	Colon Smooth Muscle	Colon
44	chr4:152129200-152138400	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr4:152129200-152142200	Weak transcription	Brain Cingulate Gyrus	brain
46	chr4:152129200-152148800	Weak transcription	Liver	Liver
47	chr4:152129400-152133400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr4:152129400-152133600	Weak transcription	Adipose Nuclei	Adipose
49	chr4:152129400-152134000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr4:152129400-152136200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links