Variant report

Variant	rs3924892
Chromosome Location	chr14:105494262-105494263
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	chr14:105441966..105444390-chr14:105493852..105497490,3	MCF-7	breast:
2	chr14:105455194..105456749-chr14:105493556..105495822,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140104	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10136586	0.88[CEU][hapmap];0.90[CHB][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10143022	0.81[CEU][hapmap];0.84[CHB][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10143079	0.88[CEU][hapmap];0.94[CHB][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10144833	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10147484	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10147672	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10162501	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11160831	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11160832	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11628967	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12431580	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28391579	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3803294	0.88[CEU][hapmap];0.90[CHB][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3923888	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4075085	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4075087	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4359376	0.84[ASN][1000 genomes]
rs4570772	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4577017	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4577018	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4635277	0.83[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];0.80[GIH][hapmap];0.97[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61996057	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61997770	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61997771	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6576069	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6576071	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6576072	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7146925	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7150715	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7157970	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7159328	0.88[CEU][hapmap];0.90[CHB][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7159532	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9324080	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9652309	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1828345	chr14:105100787-105803170	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer 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	165 gene(s)	inside rSNPs	diseases
2	nsv542225	chr14:105133688-105803170	Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
3	nsv542227	chr14:105157572-105803170	Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	147 gene(s)	inside rSNPs	diseases
4	nsv917106	chr14:105339195-105803170	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
5	nsv902419	chr14:105381763-105494262	Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh 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	59 gene(s)	inside rSNPs	diseases
6	nsv456457	chr14:105404384-105555396	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
7	nsv566141	chr14:105404384-105555396	Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
8	nsv902420	chr14:105410183-105494262	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
9	nsv902421	chr14:105410183-105574843	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
10	nsv902422	chr14:105420215-105803170	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
11	nsv1052190	chr14:105423761-105722653	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
12	nsv902423	chr14:105430890-105803170	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
13	nsv1042303	chr14:105435649-105633544	Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
14	nsv456458	chr14:105435649-105690092	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
15	nsv566150	chr14:105435649-105690092	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
16	nsv902424	chr14:105436222-105803170	Genic enhancers Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS 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	86 gene(s)	inside rSNPs	diseases
17	nsv566151	chr14:105459140-105555396	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
18	nsv456459	chr14:105459140-105617891	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
19	nsv566152	chr14:105459140-105617891	Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
20	nsv902425	chr14:105463936-105690092	Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
21	nsv983941	chr14:105485574-105534240	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3924892	KLC1	cis	parietal	SCAN
rs3924892	AHNAK2	cis	cerebellum	SCAN
rs3924892	DIO3OS	cis	parietal	SCAN
rs3924892	DYNC1H1	cis	parietal	SCAN
rs3924892	TRMT61A	cis	parietal	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:105488400-105496600	Weak transcription	Esophagus	oesophagus
2	chr14:105488400-105497400	Weak transcription	Gastric	stomach
3	chr14:105488600-105499200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr14:105488600-105499200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr14:105488800-105494800	Enhancers	HMEC	breast
6	chr14:105488800-105499000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr14:105488800-105499000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr14:105488800-105499200	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr14:105488800-105499400	Weak transcription	Pancreas	Pancrea
10	chr14:105488800-105499800	Weak transcription	Spleen	Spleen
11	chr14:105489000-105495000	Enhancers	NH-A	brain
12	chr14:105489000-105497200	Weak transcription	Fetal Heart	heart
13	chr14:105489000-105499200	Weak transcription	Primary T cells from cord blood	blood
14	chr14:105489000-105499200	Weak transcription	Fetal Intestine Small	intestine
15	chr14:105489200-105495200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr14:105489200-105499000	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr14:105489600-105499200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr14:105490200-105494600	Enhancers	NHEK	skin
19	chr14:105490600-105496400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr14:105490600-105496600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr14:105490800-105499000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr14:105491200-105495200	Enhancers	Muscle Satellite Cultured Cells	--
23	chr14:105491400-105499000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr14:105491600-105494400	Weak transcription	NHLF	lung
25	chr14:105491600-105494600	Enhancers	A549	lung
26	chr14:105492000-105494400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr14:105492000-105499200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr14:105492000-105499400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr14:105492000-105499400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr14:105492000-105499600	Weak transcription	HSMMtube	muscle
31	chr14:105492200-105499200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr14:105492600-105494400	Enhancers	Monocytes-CD14+_RO01746	blood
33	chr14:105492600-105499200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr14:105492800-105494400	Enhancers	Osteobl	bone
35	chr14:105493000-105499200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr14:105493200-105494600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr14:105493200-105495200	Enhancers	NHDF-Ad	bronchial
38	chr14:105493400-105495000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr14:105493600-105495200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr14:105493800-105494600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr14:105493800-105494800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr14:105493800-105498800	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr14:105493800-105498800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr14:105493800-105499200	Weak transcription	Primary B cells from peripheral blood	blood
45	chr14:105493800-105499200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr14:105493800-105499200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr14:105493800-105499200	Weak transcription	HUVEC	blood vessel
48	chr14:105494000-105494400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr14:105494000-105494400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr14:105494000-105495000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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