Variant report

Variant	rs6547657
Chromosome Location	chr2:86265173-86265174
allele	G/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	RCOR1	chr2:86262772-86265905	IMR90	lung:	n/a	n/a
2	MAX	chr2:86265115-86265724	GM12878	blood:	n/a	n/a
3	CTCF	chr2:86265060-86265210	HCPEpiC	choroid plexus:	n/a	chr2:86265085-86265093
4	EP300	chr2:86264991-86265935	GM12878	blood:	n/a	n/a
5	RELA	chr2:86265011-86266158	GM19099	blood:	n/a	n/a
6	WRNIP1	chr2:86265007-86266068	GM12878	blood:	n/a	n/a
7	RCOR1	chr2:86264929-86265843	GM12878	blood:	n/a	n/a
8	CHD2	chr2:86265053-86265868	GM12878	blood:	n/a	n/a
9	BHLHE40	chr2:86265032-86265761	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86263075..86266284-chr2:86266783..86270779,4	MCF-7	breast:

Variant related genes	Relation type
POLR1A	TF binding region
ENSG00000068654	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs2278086	0.96[AFR][1000 genomes]
rs2278537	1.00[AFR][1000 genomes]
rs34302587	0.93[AFR][1000 genomes]
rs35093541	0.96[AFR][1000 genomes]
rs36051710	0.96[AFR][1000 genomes]
rs3770086	1.00[AFR][1000 genomes]
rs3770091	1.00[AFR][1000 genomes]
rs56673339	1.00[AFR][1000 genomes]
rs57906735	1.00[AFR][1000 genomes]
rs58403969	1.00[AFR][1000 genomes]
rs58614836	0.89[AFR][1000 genomes]
rs59947468	0.90[AFR][1000 genomes]
rs60719866	0.96[AFR][1000 genomes]
rs60887312	0.83[AFR][1000 genomes]
rs61185790	1.00[AFR][1000 genomes]
rs6547656	1.00[AFR][1000 genomes]
rs6704777	1.00[AFR][1000 genomes]
rs6708146	1.00[AFR][1000 genomes]
rs6712535	1.00[AFR][1000 genomes]
rs6712576	1.00[AFR][1000 genomes]
rs6724612	0.93[AFR][1000 genomes]
rs6737211	1.00[AFR][1000 genomes]
rs6741815	1.00[AFR][1000 genomes]
rs6741832	1.00[AFR][1000 genomes]
rs6755224	1.00[AFR][1000 genomes]
rs6755246	0.96[AFR][1000 genomes]
rs7557349	1.00[AFR][1000 genomes]
rs7569577	1.00[AFR][1000 genomes]
rs7572206	1.00[AFR][1000 genomes]
rs7582484	1.00[AFR][1000 genomes]
rs7599656	1.00[AFR][1000 genomes]
rs7606062	0.93[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001104	chr2:86182021-86271923	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv535807	chr2:86182021-86271923	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv2751903	chr2:86253542-86505453	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS 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 miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv531380	chr2:86253552-86469217	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86251200-86273200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
2	chr2:86251200-86281400	Strong transcription	H9 Cell Line	embryonic stem cell
3	chr2:86251200-86283000	Strong transcription	HepG2	liver
4	chr2:86251200-86283200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:86251200-86285000	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr2:86251200-86285200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr2:86252000-86331200	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr2:86252200-86282600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr2:86252200-86285200	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr2:86252400-86283200	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr2:86252600-86267800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
12	chr2:86252600-86276800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:86258200-86265400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr2:86260200-86266200	Genic enhancers	Fetal Stomach	stomach
15	chr2:86260600-86268800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr2:86260600-86269000	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr2:86260800-86268800	Weak transcription	Ovary	ovary
18	chr2:86261200-86272000	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr2:86261400-86265600	Enhancers	Left Ventricle	heart
20	chr2:86261400-86266200	Enhancers	Psoas Muscle	Psoas
21	chr2:86261600-86265600	Enhancers	Right Ventricle	heart
22	chr2:86261800-86266400	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr2:86262000-86265800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr2:86262400-86265200	Enhancers	Spleen	Spleen
25	chr2:86262400-86265200	Genic enhancers	NHEK	skin
26	chr2:86262400-86266000	Genic enhancers	Brain Angular Gyrus	brain
27	chr2:86262400-86266000	Genic enhancers	Fetal Intestine Small	intestine
28	chr2:86262400-86266000	Enhancers	Right Atrium	heart
29	chr2:86262400-86266200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr2:86262400-86266200	Enhancers	Lung	lung
31	chr2:86262400-86266800	Genic enhancers	Placenta	Placenta
32	chr2:86262400-86268400	Flanking Active TSS	Thymus	Thymus
33	chr2:86262600-86265200	Enhancers	Fetal Kidney	kidney
34	chr2:86262600-86265600	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr2:86262600-86265600	Genic enhancers	Brain Germinal Matrix	brain
36	chr2:86262600-86265600	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr2:86262600-86265800	Enhancers	Colon Smooth Muscle	Colon
38	chr2:86262600-86265800	Enhancers	Small Intestine	intestine
39	chr2:86262600-86266200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr2:86262600-86266200	Enhancers	Stomach Mucosa	stomach
41	chr2:86262600-86266200	Genic enhancers	NHLF	lung
42	chr2:86262600-86267000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr2:86262800-86265200	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr2:86262800-86265200	Flanking Active TSS	Dnd41	blood
45	chr2:86262800-86265400	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:86262800-86265400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr2:86262800-86265400	Genic enhancers	Fetal Intestine Large	intestine
48	chr2:86262800-86265400	Enhancers	NHDF-Ad	bronchial
49	chr2:86262800-86265600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
50	chr2:86262800-86266000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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