Variant report

Variant	rs11682994
Chromosome Location	chr2:97425561-97425562
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:14)
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	NRF1	chr2:97425561-97425642	GM12878	blood:	n/a	n/a
2	CTCF	chr2:97425480-97425630	K562	blood:	n/a	chr2:97425536-97425549

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:97407779..97410358-chr2:97422374..97426417,4	K562	blood:
2	chr2:97399050..97401934-chr2:97425434..97428071,2	MCF-7	breast:
3	chr2:97268720..97275117-chr2:97424272..97429412,8	MCF-7	breast:
4	chr2:97358845..97361710-chr2:97424992..97426847,2	K562	blood:
5	chr2:97425294..97427081-chr2:97533526..97535772,2	K562	blood:
6	chr2:97299733..97305587-chr2:97425305..97429139,7	K562	blood:
7	chr2:97299733..97305587-chr2:97422203..97428186,8	K562	blood:
8	chr2:97422064..97424734-chr2:97424939..97426592,2	MCF-7	breast:
9	chr2:97403401..97407119-chr2:97425023..97428100,7	MCF-7	breast:
10	chr2:97402906..97407899-chr2:97425229..97430147,10	MCF-7	breast:
11	chr19:59057645..59060088-chr2:97425289..97427469,2	MCF-7	breast:
12	chr2:97405153..97407675-chr2:97425109..97427390,3	K562	blood:
13	chr2:97423625..97426138-chr2:97484337..97486226,2	K562	blood:
14	chr2:97413080..97414856-chr2:97424124..97425646,2	K562	blood:

No data

Variant related genes	Relation type
CNNM4	TF binding region
ENSG00000114988	Chromatin interaction
ENSG00000168758	Chromatin interaction
ENSG00000130726	Chromatin interaction
ENSG00000114982	Chromatin interaction
ENSG00000249715	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10189727	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.88[ASN][1000 genomes]
rs1257020	1.00[YRI][hapmap]
rs1318597	0.95[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs1624844	1.00[YRI][hapmap]
rs1796046	1.00[YRI][hapmap]
rs2280355	0.85[CEU][hapmap];0.97[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs2314398	0.81[JPT][hapmap]
rs2678385	0.85[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4907251	0.82[JPT][hapmap];1.00[LWK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs6576983	0.93[ASN][1000 genomes]
rs6576984	0.95[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs6576993	1.00[YRI][hapmap]
rs6707255	1.00[YRI][hapmap]
rs6727384	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6730773	0.95[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs6741561	0.93[ASN][1000 genomes]
rs68026712	0.96[ASN][1000 genomes]
rs72941253	0.89[ASN][1000 genomes]
rs7582249	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap];0.92[ASN][1000 genomes]
rs7586317	0.95[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs7608661	0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs878919	0.98[ASN][1000 genomes]
rs968470	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9789421	0.80[AFR][1000 genomes]
rs994430	0.95[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	esv3460902	chr2:97138421-97459342	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	esv3460903	chr2:97138421-97459342	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
9	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
10	nsv834307	chr2:97321447-97479266	Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
11	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
12	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
13	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
14	esv3438902	chr2:97425450-97427998	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11682994	LOC728537	cis	brain	BrainEAC
rs11682994	LMAN2L	cis	cerebellum	SCAN
rs11682994	KIAA1310	cis	parietal	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97420600-97425800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr2:97420600-97426000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr2:97420600-97426000	Weak transcription	Osteobl	bone
4	chr2:97422800-97425800	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr2:97423200-97426000	Enhancers	Fetal Intestine Small	intestine
6	chr2:97423600-97426000	Enhancers	Duodenum Mucosa	Duodenum
7	chr2:97423600-97426000	Enhancers	Fetal Intestine Large	intestine
8	chr2:97423800-97426200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr2:97424200-97425800	Weak transcription	HMEC	breast
10	chr2:97424200-97426000	Weak transcription	Liver	Liver
11	chr2:97424400-97425600	Weak transcription	Fetal Kidney	kidney
12	chr2:97424400-97425800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr2:97424600-97426000	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr2:97424600-97426000	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr2:97424600-97426000	Enhancers	Stomach Mucosa	stomach
16	chr2:97424800-97425800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:97424800-97425800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr2:97424800-97425800	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr2:97424800-97425800	Enhancers	A549	lung
20	chr2:97424800-97426000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr2:97424800-97426000	Enhancers	Primary T cells fromperipheralblood	blood
22	chr2:97424800-97426000	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr2:97424800-97426000	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr2:97424800-97426000	Enhancers	Brain Cingulate Gyrus	brain
25	chr2:97424800-97426000	Enhancers	GM12878-XiMat	blood
26	chr2:97424800-97426000	Enhancers	K562	blood
27	chr2:97424800-97426200	Enhancers	Esophagus	oesophagus
28	chr2:97425000-97425600	Flanking Bivalent TSS/Enh	HepG2	liver
29	chr2:97425000-97425800	Enhancers	Primary hematopoietic stem cells	blood
30	chr2:97425000-97425800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr2:97425000-97425800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr2:97425000-97426000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr2:97425000-97426000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr2:97425000-97426000	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr2:97425000-97426000	Enhancers	Primary B cells from peripheral blood	blood
36	chr2:97425000-97426000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr2:97425000-97426000	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr2:97425000-97426000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr2:97425000-97426000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
40	chr2:97425000-97426000	Enhancers	Colonic Mucosa	Colon
41	chr2:97425000-97426000	Enhancers	Rectal Mucosa Donor 29	rectum
42	chr2:97425000-97426200	Enhancers	Sigmoid Colon	Sigmoid Colon
43	chr2:97425000-97426400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr2:97425200-97425600	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr2:97425200-97425600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
46	chr2:97425200-97425600	Enhancers	Dnd41	blood
47	chr2:97425200-97425800	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr2:97425200-97425800	Active TSS	Stomach Smooth Muscle	stomach
49	chr2:97425200-97426000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr2:97425200-97426000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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