Variant report

Variant	rs11678174
Chromosome Location	chr2:97249103-97249104
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	chr2:97247336..97249480-chr2:97253671..97255263,2	MCF-7	breast:
2	chr2:97248384..97250902-chr2:97301797..97304006,3	K562	blood:

Variant related genes	Relation type
ENSG00000114982	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10460601	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164109	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11677722	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11682934	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11691670	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12469420	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12471390	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12477059	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2278563	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4907237	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4907240	0.92[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4907241	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4907242	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4907246	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62154845	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62156200	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs66727130	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6747149	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6749159	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6759099	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7575254	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7580048	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7600903	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv999871	chr2:97157196-97407711	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv535829	chr2:97157196-97407711	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv469775	chr2:97240926-97412491	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh 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	23 gene(s)	inside rSNPs	diseases
12	nsv482586	chr2:97240926-97412491	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS 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 target site	23 gene(s)	inside rSNPs	diseases
13	nsv834306	chr2:97241115-97412938	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11678174	CIAO1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97220400-97258000	Weak transcription	Ovary	ovary
2	chr2:97220600-97257000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr2:97220800-97257400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr2:97223800-97256000	Weak transcription	Fetal Intestine Small	intestine
5	chr2:97228800-97255200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr2:97231600-97250200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr2:97233000-97257800	Weak transcription	Gastric	stomach
8	chr2:97234600-97258200	Weak transcription	Aorta	Aorta
9	chr2:97235200-97250000	Weak transcription	Fetal Brain Female	brain
10	chr2:97235600-97249800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr2:97237000-97257000	Weak transcription	Brain Hippocampus Middle	brain
12	chr2:97237600-97249800	Weak transcription	Left Ventricle	heart
13	chr2:97237800-97257800	Weak transcription	Thymus	Thymus
14	chr2:97238000-97257000	Weak transcription	Fetal Lung	lung
15	chr2:97238200-97258200	Weak transcription	Spleen	Spleen
16	chr2:97238400-97257400	Weak transcription	Fetal Muscle Leg	muscle
17	chr2:97239000-97257400	Weak transcription	Brain Anterior Caudate	brain
18	chr2:97239200-97253000	Weak transcription	Lung	lung
19	chr2:97239400-97249800	Weak transcription	Adipose Nuclei	Adipose
20	chr2:97239400-97252800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr2:97239400-97257600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr2:97239600-97251800	Weak transcription	Fetal Stomach	stomach
23	chr2:97239600-97258800	Weak transcription	Right Ventricle	heart
24	chr2:97241400-97257400	Weak transcription	Fetal Intestine Large	intestine
25	chr2:97242400-97250200	Weak transcription	Duodenum Mucosa	Duodenum
26	chr2:97242400-97258200	Weak transcription	Brain Cingulate Gyrus	brain
27	chr2:97242600-97257600	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr2:97243600-97257800	Weak transcription	HepG2	liver
29	chr2:97243800-97257800	Weak transcription	Brain Substantia Nigra	brain
30	chr2:97244000-97257400	Weak transcription	Primary T cells from cord blood	blood
31	chr2:97244600-97257400	Weak transcription	HSMMtube	muscle
32	chr2:97244800-97258000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr2:97244800-97259400	Weak transcription	Stomach Mucosa	stomach
34	chr2:97245000-97255000	Weak transcription	A549	lung
35	chr2:97245000-97257400	Weak transcription	Primary hematopoietic stem cells	blood
36	chr2:97245600-97252800	Weak transcription	Psoas Muscle	Psoas
37	chr2:97245600-97258200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr2:97246000-97252800	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr2:97246400-97257200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr2:97246800-97257400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr2:97246800-97258800	Weak transcription	Pancreas	Pancrea
42	chr2:97246800-97259200	Weak transcription	Fetal Brain Male	brain
43	chr2:97247000-97258200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr2:97247200-97256600	Weak transcription	Placenta	Placenta
45	chr2:97247200-97256800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr2:97247200-97259200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr2:97247400-97257800	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr2:97247600-97249200	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr2:97247600-97257400	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr2:97247600-97258200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links