Variant report

Variant	rs11886360
Chromosome Location	chr2:97488714-97488715
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:97488647-97489600	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:97488688-97489556	Hela-S3	cervix:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr2:97426560..97429669-chr2:97487357..97491316,3	MCF-7	breast:
2	chr2:97481554..97483965-chr2:97485690..97489331,4	K562	blood:
3	chr2:97485243..97487590-chr2:97488135..97490433,3	K562	blood:
4	chr2:97488123..97491381-chr2:97522097..97525123,6	MCF-7	breast:
5	chr2:97488060..97490357-chr2:97534412..97536411,3	MCF-7	breast:

No data

Variant related genes	Relation type
CNNM3	TF binding region
ENSG00000158158	Chromatin interaction
ENSG00000213337	Chromatin interaction
ENSG00000163126	Chromatin interaction
ENSG00000168758	Chromatin interaction
ENSG00000168763	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1047634	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11892821	0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1878656	0.80[YRI][hapmap]
rs2314649	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34013660	1.00[EUR][1000 genomes]
rs56129857	1.00[EUR][1000 genomes]
rs58448521	1.00[EUR][1000 genomes]
rs6576977	1.00[EUR][1000 genomes]
rs6576985	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6576988	0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6576991	1.00[EUR][1000 genomes]
rs6707008	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6713046	1.00[EUR][1000 genomes]
rs6733826	1.00[EUR][1000 genomes]
rs6744498	1.00[EUR][1000 genomes]
rs6746421	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6748214	1.00[EUR][1000 genomes]
rs6748234	0.91[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6759613	1.00[EUR][1000 genomes]
rs72945119	1.00[EUR][1000 genomes]
rs73960684	1.00[EUR][1000 genomes]
rs7565577	0.91[YRI][hapmap];0.83[AFR][1000 genomes]
rs7569178	1.00[EUR][1000 genomes]
rs7570831	1.00[EUR][1000 genomes]
rs7580104	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7581456	0.91[YRI][hapmap];0.83[AFR][1000 genomes]
rs7587149	1.00[EUR][1000 genomes]
rs7589082	0.91[YRI][hapmap]
rs7593340	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv874680	chr2:97309574-97678319	Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
8	nsv526313	chr2:97333492-97660619	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
9	nsv874681	chr2:97410949-97577343	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
10	nsv874682	chr2:97423626-97567389	Transcr. at gene 5' and 3' Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
11	nsv1009720	chr2:97464803-97522856	Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
12	nsv535830	chr2:97464803-97522856	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97483000-97490800	Enhancers	Fetal Heart	heart
2	chr2:97483600-97490000	Weak transcription	NH-A	brain
3	chr2:97483600-97492200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr2:97483600-97493400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr2:97483600-97493400	Weak transcription	HSMMtube	muscle
6	chr2:97483600-97498200	Weak transcription	HSMM	muscle
7	chr2:97483800-97490000	Genic enhancers	Fetal Muscle Leg	muscle
8	chr2:97483800-97492200	Weak transcription	NHLF	lung
9	chr2:97483800-97493200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr2:97483800-97493400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr2:97483800-97493600	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr2:97483800-97494400	Weak transcription	Osteobl	bone
13	chr2:97483800-97498400	Weak transcription	NHDF-Ad	bronchial
14	chr2:97484000-97493200	Weak transcription	Fetal Kidney	kidney
15	chr2:97484000-97493600	Weak transcription	NHEK	skin
16	chr2:97484400-97489400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
17	chr2:97484600-97489400	Genic enhancers	Fetal Thymus	thymus
18	chr2:97484600-97518400	Weak transcription	HUVEC	blood vessel
19	chr2:97484800-97493600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr2:97485200-97490800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr2:97485200-97490800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:97485200-97498400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:97485600-97493400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr2:97485800-97490600	Genic enhancers	Fetal Intestine Small	intestine
25	chr2:97486000-97505000	Strong transcription	Fetal Stomach	stomach
26	chr2:97486200-97488800	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr2:97486200-97489400	Weak transcription	A549	lung
28	chr2:97486600-97488800	Weak transcription	Esophagus	oesophagus
29	chr2:97486600-97489000	Weak transcription	Colonic Mucosa	Colon
30	chr2:97486600-97489200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr2:97486600-97490800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr2:97486600-97491600	Weak transcription	Primary B cells from cord blood	blood
33	chr2:97486600-97492200	Weak transcription	K562	blood
34	chr2:97486600-97492600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:97486600-97498000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr2:97486800-97488800	Weak transcription	Adipose Nuclei	Adipose
37	chr2:97486800-97490800	Weak transcription	Primary hematopoietic stem cells	blood
38	chr2:97486800-97500800	Strong transcription	Thymus	Thymus
39	chr2:97487000-97498800	Strong transcription	Primary B cells from peripheral blood	blood
40	chr2:97487200-97489800	Genic enhancers	Fetal Brain Female	brain
41	chr2:97487200-97490400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr2:97487200-97490600	Genic enhancers	HepG2	liver
43	chr2:97487200-97490800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr2:97487200-97491200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr2:97487200-97501800	Strong transcription	Primary T cells from cord blood	blood
46	chr2:97487200-97504000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr2:97487400-97488800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr2:97487400-97488800	Enhancers	Liver	Liver
49	chr2:97487400-97489000	Weak transcription	Psoas Muscle	Psoas
50	chr2:97487400-97489200	Weak transcription	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links