Variant report

Variant	rs6726941
Chromosome Location	chr2:47184447-47184448
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr2:47184067-47184791	MCF-7	breast:	n/a	n/a
2	REST	chr2:47184331-47184764	MCF-7	breast:	n/a	n/a
3	MAX	chr2:47184028-47184718	MCF-7	breast:	n/a	n/a
4	FOXA1	chr2:47184126-47184491	T-47D	breast:	n/a	chr2:47184300-47184315
5	FOXA2	chr2:47183999-47184640	A549	lung:	n/a	n/a
6	HDAC2	chr2:47184144-47184763	MCF-7	breast:	n/a	n/a
7	NR2F2	chr2:47184055-47184782	MCF-7	breast:	n/a	n/a
8	CEBPB	chr2:47184118-47184761	MCF-7	breast:	n/a	chr2:47184511-47184524
9	FOXA2	chr2:47184017-47184523	A549	lung:	n/a	n/a
10	FOXM1	chr2:47184088-47184753	MCF-7	breast:	n/a	n/a
11	GATA3	chr2:47184219-47184658	MCF-7	breast:	n/a	n/a
12	NR2F2	chr2:47183896-47184990	MCF-7	breast:	n/a	n/a
13	ESR1	chr2:47184190-47184589	T-47D	breast:	n/a	n/a
14	EP300	chr2:47183986-47184788	MCF-7	breast:	n/a	n/a
15	POLR2A	chr2:47184307-47184507	HepG2	liver:	n/a	n/a
16	FOXA1	chr2:47184189-47184457	T-47D	breast:	n/a	chr2:47184300-47184315

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:47168340..47172583-chr2:47183123..47189203,6	MCF-7	breast:
2	chr2:47184299..47184895-chr2:47197606..47198181,3	MCF-7	breast:
3	chr2:47184160..47184888-chr2:47197610..47198458,4	MCF-7	breast:
4	chr2:47174154..47179572-chr2:47181486..47185069,4	MCF-7	breast:
5	chr2:47184424..47187417-chr2:47402642..47404975,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000272814	TF binding region
ENSG00000068724	Chromatin interaction
ENSG00000180398	Chromatin interaction
ENSG00000143933	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs13399571	1.00[CEU][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17036022	0.82[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17036033	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17036039	1.00[CHD][hapmap]
rs17480869	0.86[ASN][1000 genomes]
rs17480988	0.86[ASN][1000 genomes]
rs17481037	0.86[ASN][1000 genomes]
rs17481209	0.86[ASN][1000 genomes]
rs17540157	0.86[ASN][1000 genomes]
rs17540219	0.86[ASN][1000 genomes]
rs17540462	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3814035	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55641002	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55805005	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55824224	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58637066	0.86[ASN][1000 genomes]
rs58674434	0.86[ASN][1000 genomes]
rs59785154	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60732316	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6727430	0.86[ASN][1000 genomes]
rs6727529	0.86[ASN][1000 genomes]
rs6751599	0.86[ASN][1000 genomes]
rs6751621	1.00[CEU][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6754795	0.86[ASN][1000 genomes]
rs6755001	0.86[ASN][1000 genomes]
rs72806525	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72806536	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72806537	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72806538	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72806541	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72806558	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72806562	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72806571	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7564728	0.86[ASN][1000 genomes]
rs7576915	1.00[CHD][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
5	nsv524970	chr2:47162739-47302095	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47169800-47214600	Weak transcription	Fetal Kidney	kidney
2	chr2:47173000-47191800	Weak transcription	Fetal Brain Male	brain
3	chr2:47174400-47212400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr2:47176400-47192600	Strong transcription	Dnd41	blood
5	chr2:47177200-47185000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr2:47177200-47210400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr2:47177400-47192800	Strong transcription	Fetal Stomach	stomach
8	chr2:47177600-47188200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr2:47177600-47190000	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr2:47177600-47191200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr2:47178400-47188000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr2:47178400-47192800	Strong transcription	Thymus	Thymus
13	chr2:47178600-47189800	Strong transcription	Primary T helper cells PMA-I stimulated	--
14	chr2:47178800-47189400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr2:47178800-47190000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr2:47178800-47191400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr2:47179000-47188200	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr2:47179000-47191000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr2:47179000-47192800	Strong transcription	Primary T cells from cord blood	blood
20	chr2:47179200-47195000	Strong transcription	Fetal Thymus	thymus
21	chr2:47179400-47189600	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr2:47179400-47191400	Strong transcription	Primary hematopoietic stem cells	blood
23	chr2:47179400-47192200	Strong transcription	Primary B cells from cord blood	blood
24	chr2:47179400-47192600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr2:47179400-47193800	Strong transcription	Primary B cells from peripheral blood	blood
26	chr2:47179800-47189400	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr2:47180800-47188000	Strong transcription	Fetal Lung	lung
28	chr2:47181200-47192200	Strong transcription	GM12878-XiMat	blood
29	chr2:47181600-47210800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr2:47181800-47185800	Enhancers	Liver	Liver
31	chr2:47182200-47184600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr2:47182600-47187200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr2:47182600-47189800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr2:47182600-47190400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr2:47182800-47187400	Strong transcription	Fetal Brain Female	brain
36	chr2:47182800-47188400	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr2:47182800-47189600	Strong transcription	Fetal Muscle Leg	muscle
38	chr2:47183000-47187400	Strong transcription	Brain Angular Gyrus	brain
39	chr2:47183000-47187600	Strong transcription	Rectal Smooth Muscle	rectum
40	chr2:47183000-47187600	Genic enhancers	A549	lung
41	chr2:47183000-47188000	Strong transcription	Brain Substantia Nigra	brain
42	chr2:47183000-47188000	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr2:47183000-47189800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr2:47183000-47189800	Weak transcription	K562	blood
45	chr2:47183000-47192000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr2:47183000-47195000	Weak transcription	Small Intestine	intestine
47	chr2:47183200-47185600	Strong transcription	NHEK	skin
48	chr2:47183200-47186600	Strong transcription	Hela-S3	cervix
49	chr2:47183200-47186600	Strong transcription	NH-A	brain
50	chr2:47183200-47187200	Strong transcription	Esophagus	oesophagus

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