Variant report

Variant	rs10743758
Chromosome Location	chr12:31652081-31652082
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:31645681..31648505-chr12:31649831..31652317,2	MCF-7	breast:
2	chr12:31477853..31479462-chr12:31651930..31653827,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139146	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1012154	0.81[CHB][hapmap];0.81[CHD][hapmap]
rs10743757	0.94[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.98[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs10771832	1.00[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap];0.84[YRI][hapmap]
rs10843947	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.85[YRI][hapmap]
rs11051418	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs11051437	0.92[CEU][hapmap];0.93[CHB][hapmap];0.92[YRI][hapmap]
rs11051441	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.98[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1150953	0.81[CHB][hapmap]
rs11615961	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap]
rs1259235	0.81[CHB][hapmap];0.81[CHD][hapmap]
rs1259236	0.84[CEU][hapmap];0.93[CHB][hapmap]
rs1259428	0.92[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.91[TSI][hapmap]
rs1259432	0.93[CHB][hapmap]
rs1469673	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap]
rs1716216	0.81[CHB][hapmap]
rs2116704	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap]
rs2568884	0.81[CHB][hapmap];0.85[CHD][hapmap];0.84[TSI][hapmap]
rs2617200	0.81[CHB][hapmap]
rs2682697	0.82[CEU][hapmap]
rs3844573	0.89[CEU][hapmap];0.93[CHB][hapmap];0.85[YRI][hapmap]
rs3850965	0.89[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.80[LWK][hapmap];0.89[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap]
rs3898368	0.88[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.95[LWK][hapmap];0.89[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs4482118	0.83[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.98[LWK][hapmap];0.89[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs4931501	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.93[YRI][hapmap]
rs4931507	0.89[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.82[LWK][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap]
rs6487992	0.92[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];0.86[YRI][hapmap]
rs708209	0.92[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.89[TSI][hapmap]
rs7133082	0.96[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.86[YRI][hapmap]
rs7135856	0.91[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.92[YRI][hapmap]
rs7136476	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[YRI][hapmap]
rs7294574	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.91[LWK][hapmap];0.89[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap]
rs7302698	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.86[YRI][hapmap]
rs7307616	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.86[YRI][hapmap]
rs7313118	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.98[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs793176	0.80[CHB][hapmap]
rs793184	0.82[CEU][hapmap]
rs7954595	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.86[YRI][hapmap]
rs7957026	1.00[CEU][hapmap];0.81[GIH][hapmap];0.98[TSI][hapmap]
rs7959877	0.83[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.98[LWK][hapmap];0.89[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap]
rs7962896	0.83[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.98[LWK][hapmap];0.89[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap]
rs7974437	0.94[CHB][hapmap];0.96[CHD][hapmap];0.82[JPT][hapmap]
rs7975761	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap]
rs7976644	0.83[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.98[LWK][hapmap];0.89[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs899159	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041877	chr12:31009451-31809254	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv541440	chr12:31009451-31809254	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	esv2751046	chr12:31174233-31684733	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv1836923	chr12:31539122-31761172	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
6	nsv898965	chr12:31631819-31771689	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv832365	chr12:31642811-31808532	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10743758	FLJ13224	cis	cerebellum	SCAN
rs10743758	DENND5B	cis	cerebellum	SCAN
rs10743758	DENND5B	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31583400-31662000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:31628800-31655800	Weak transcription	Gastric	stomach
3	chr12:31630400-31655000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr12:31633000-31652400	Weak transcription	Fetal Brain Female	brain
5	chr12:31633200-31652200	Weak transcription	Adipose Nuclei	Adipose
6	chr12:31636200-31663000	Weak transcription	Aorta	Aorta
7	chr12:31639000-31655800	Weak transcription	Left Ventricle	heart
8	chr12:31642600-31670000	Weak transcription	Fetal Lung	lung
9	chr12:31643600-31658800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr12:31644400-31659400	Weak transcription	Pancreas	Pancrea
11	chr12:31645600-31658000	Weak transcription	Fetal Intestine Small	intestine
12	chr12:31646000-31652400	Weak transcription	Fetal Kidney	kidney
13	chr12:31646000-31652600	Weak transcription	Brain Hippocampus Middle	brain
14	chr12:31646000-31659400	Weak transcription	NH-A	brain
15	chr12:31646000-31659800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:31646200-31652600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr12:31646200-31657400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr12:31647000-31652200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr12:31647400-31660000	Weak transcription	Psoas Muscle	Psoas
20	chr12:31647600-31652600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr12:31647600-31661200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr12:31647800-31653400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr12:31647800-31661400	Weak transcription	Brain Angular Gyrus	brain
24	chr12:31648800-31652200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr12:31648800-31657200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:31649000-31654000	Weak transcription	Primary B cells from cord blood	blood
27	chr12:31649200-31653800	Weak transcription	Primary B cells from peripheral blood	blood
28	chr12:31649400-31652200	Weak transcription	Brain Anterior Caudate	brain
29	chr12:31649400-31654800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr12:31649400-31656600	Weak transcription	NHEK	skin
31	chr12:31649800-31653200	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr12:31650000-31653000	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr12:31650000-31653000	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr12:31650000-31653200	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr12:31650200-31653000	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr12:31650200-31653000	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr12:31650600-31652400	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr12:31650800-31655800	Weak transcription	Ovary	ovary
39	chr12:31650800-31660800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr12:31651000-31653000	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr12:31651000-31653200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr12:31651200-31652200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr12:31651200-31653200	Enhancers	HUVEC	blood vessel
44	chr12:31651200-31656200	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr12:31651400-31653800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr12:31651600-31652200	Enhancers	A549	lung
47	chr12:31651600-31652600	Weak transcription	Rectal Smooth Muscle	rectum
48	chr12:31651600-31655800	Weak transcription	Liver	Liver
49	chr12:31651600-31661400	Weak transcription	HepG2	liver
50	chr12:31651600-31661800	Weak transcription	Colon Smooth Muscle	Colon

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