Variant report

Variant	rs12355439
Chromosome Location	chr10:52135089-52135090
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:52127857..52130924-chr10:52133934..52136011,3	K562	blood:
2	chr10:52127640..52130879-chr10:52134264..52136292,3	K562	blood:
3	chr10:52128591..52131322-chr10:52132559..52135165,2	MCF-7	breast:
4	chr10:52133378..52136507-chr10:52147936..52151266,3	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10443954	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10508926	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[TSI][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10508929	0.86[YRI][hapmap]
rs10740666	1.00[CHB][hapmap]
rs10825903	0.87[CEU][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10826032	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10826101	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11005316	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11005345	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11005502	1.00[CHB][hapmap]
rs11005595	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11005612	0.87[EUR][1000 genomes]
rs11005708	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11005730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes]
rs11005872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11005877	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11005882	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11005952	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11005956	1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006012	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11516712	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11591645	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11595661	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11598794	1.00[ASN][1000 genomes]
rs12354779	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12356013	1.00[CHB][hapmap]
rs12357733	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12358247	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12360058	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2177372	1.00[ASN][1000 genomes]
rs56251625	1.00[ASN][1000 genomes]
rs57959812	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58969905	1.00[ASN][1000 genomes]
rs61739586	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7071001	0.93[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7078940	0.93[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7082728	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7091881	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7096968	1.00[CEU][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74131268	1.00[ASN][1000 genomes]
rs74131270	1.00[ASN][1000 genomes]
rs74131283	1.00[ASN][1000 genomes]
rs74131284	1.00[ASN][1000 genomes]
rs74132707	0.87[EUR][1000 genomes]
rs74132723	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7477280	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518071	chr10:51595893-52157935	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1053903	chr10:51886486-52163991	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1040661	chr10:51886486-52164585	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1051028	chr10:51886486-52164585	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1037118	chr10:51886486-52167442	Enhancers ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	esv2830205	chr10:51978430-52135215	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
12	nsv1046850	chr10:52009869-52135542	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
13	nsv540625	chr10:52009869-52135542	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
14	nsv521273	chr10:52051645-52197847	Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
15	nsv430231	chr10:52119046-52163531	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
16	nsv948006	chr10:52127164-52177684	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12355439	FRMPD2	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52104000-52141400	Weak transcription	Pancreas	Pancrea
2	chr10:52104200-52157000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr10:52115800-52142200	Weak transcription	Fetal Intestine Small	intestine
4	chr10:52119400-52136000	Weak transcription	Fetal Brain Male	brain
5	chr10:52120600-52141400	Weak transcription	HSMM	muscle
6	chr10:52121200-52136600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr10:52121200-52141600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr10:52121400-52139400	Weak transcription	Placenta	Placenta
9	chr10:52123400-52136800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr10:52124600-52139400	Weak transcription	Primary B cells from cord blood	blood
11	chr10:52129000-52141600	Weak transcription	Hela-S3	cervix
12	chr10:52132400-52135200	Enhancers	Brain Hippocampus Middle	brain
13	chr10:52132800-52135200	Enhancers	Brain Cingulate Gyrus	brain
14	chr10:52132800-52135400	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr10:52132800-52135400	Enhancers	Brain Substantia Nigra	brain
16	chr10:52132800-52135600	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr10:52132800-52135600	Genic enhancers	K562	blood
18	chr10:52133000-52135400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr10:52133000-52135400	Enhancers	Duodenum Smooth Muscle	Duodenum
20	chr10:52133000-52135400	Enhancers	NHDF-Ad	bronchial
21	chr10:52133000-52135600	Enhancers	Fetal Kidney	kidney
22	chr10:52133000-52136200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr10:52133200-52135400	Enhancers	Colon Smooth Muscle	Colon
24	chr10:52133200-52142400	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr10:52133400-52135200	Enhancers	Adipose Nuclei	Adipose
26	chr10:52133400-52135400	Enhancers	Rectal Smooth Muscle	rectum
27	chr10:52133600-52136000	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr10:52133600-52146800	Weak transcription	Stomach Mucosa	stomach
29	chr10:52133800-52135200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr10:52133800-52136600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr10:52134000-52135200	Enhancers	Brain Anterior Caudate	brain
32	chr10:52134000-52135200	Enhancers	Right Atrium	heart
33	chr10:52134000-52135400	Enhancers	Primary T cells fromperipheralblood	blood
34	chr10:52134000-52135400	Enhancers	Esophagus	oesophagus
35	chr10:52134000-52135400	Enhancers	Left Ventricle	heart
36	chr10:52134000-52135400	Enhancers	Right Ventricle	heart
37	chr10:52134000-52135600	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr10:52134000-52135600	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr10:52134000-52135800	Enhancers	Primary neutrophils fromperipheralblood	blood
40	chr10:52134000-52135800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr10:52134000-52136200	Enhancers	Liver	Liver
42	chr10:52134200-52135400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr10:52134200-52135800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr10:52134200-52139400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr10:52134400-52135400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr10:52134400-52135400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr10:52134400-52135400	Enhancers	Placenta Amnion	Placenta Amnion
48	chr10:52134400-52135600	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr10:52134400-52135600	Enhancers	Primary B cells from peripheral blood	blood
50	chr10:52134400-52135600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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