Variant report

Variant	rs998871
Chromosome Location	chr14:55918302-55918303
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:55913503..55916476-chr14:55916660..55918746,2	K562	blood:
2	chr14:55917476..55919752-chr14:55927927..55929751,2	MCF-7	breast:
3	chr14:55911475..55914836-chr14:55916178..55919121,4	MCF-7	breast:
4	chr14:55912884..55915003-chr14:55916118..55918746,2	K562	blood:

Extended variants
information (count: 81 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10131672	0.81[ASN][1000 genomes]
rs10134905	0.97[ASN][1000 genomes]
rs10137395	0.97[ASN][1000 genomes]
rs10144034	0.97[ASN][1000 genomes]
rs10144130	0.80[ASN][1000 genomes]
rs10146713	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10150596	0.97[ASN][1000 genomes]
rs10150617	0.81[ASN][1000 genomes]
rs11158040	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11627405	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11627790	0.92[ASN][1000 genomes]
rs11845228	0.91[ASN][1000 genomes]
rs12431542	0.97[ASN][1000 genomes]
rs12886860	0.91[ASN][1000 genomes]
rs12887653	0.96[ASN][1000 genomes]
rs12887846	0.84[ASN][1000 genomes]
rs12888181	0.97[ASN][1000 genomes]
rs12888191	0.91[ASN][1000 genomes]
rs12888234	0.96[ASN][1000 genomes]
rs12888361	0.97[ASN][1000 genomes]
rs1572613	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs1953740	0.81[JPT][hapmap]
rs2152975	0.97[ASN][1000 genomes]
rs2152976	0.97[ASN][1000 genomes]
rs2185036	0.96[ASN][1000 genomes]
rs2341537	0.81[JPT][hapmap]
rs2341538	0.85[JPT][hapmap]
rs28478984	0.96[ASN][1000 genomes]
rs34652660	0.82[ASN][1000 genomes]
rs4243600	0.97[ASN][1000 genomes]
rs4898864	0.88[ASN][1000 genomes]
rs4898865	0.96[ASN][1000 genomes]
rs4901560	0.81[JPT][hapmap]
rs4901561	0.81[JPT][hapmap];0.82[YRI][hapmap]
rs4901562	0.85[JPT][hapmap]
rs4901563	0.97[ASN][1000 genomes]
rs4901564	0.97[ASN][1000 genomes]
rs4901565	0.96[ASN][1000 genomes]
rs4901566	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4901567	0.80[ASN][1000 genomes]
rs4901568	0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs4901569	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4901570	0.97[ASN][1000 genomes]
rs61976569	0.90[ASN][1000 genomes]
rs61976570	0.94[ASN][1000 genomes]
rs61976571	0.97[ASN][1000 genomes]
rs6573028	0.97[ASN][1000 genomes]
rs6573029	0.81[ASN][1000 genomes]
rs6573030	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6573031	0.97[ASN][1000 genomes]
rs6573032	0.97[ASN][1000 genomes]
rs6573033	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7142204	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs7143800	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7146080	0.90[ASN][1000 genomes]
rs7146170	0.97[ASN][1000 genomes]
rs7146269	0.94[ASN][1000 genomes]
rs7146306	0.89[ASN][1000 genomes]
rs7146472	0.94[ASN][1000 genomes]
rs7147968	0.96[ASN][1000 genomes]
rs7148481	0.97[ASN][1000 genomes]
rs7149317	0.85[JPT][hapmap]
rs7149622	0.97[ASN][1000 genomes]
rs8009706	0.97[ASN][1000 genomes]
rs8014621	0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs8019080	0.81[JPT][hapmap]
rs8019209	0.81[JPT][hapmap]
rs8019270	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8020152	0.97[ASN][1000 genomes]
rs955256	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs955257	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9635232	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv901958	chr14:55822095-56045411	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS 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 target site	20 gene(s)	inside rSNPs	diseases
2	nsv901960	chr14:55853724-56085130	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv901961	chr14:55853724-56101879	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv901962	chr14:55862956-56101879	Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv901963	chr14:55871452-56085130	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv901964	chr14:55871452-56101879	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
7	nsv564874	chr14:55879685-56027815	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv1051564	chr14:55895610-56130788	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv542103	chr14:55895610-56130788	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs998871	KIAA0586	cis	cerebellum	SCAN
rs998871	EXOC5	cis	parietal	SCAN
rs998871	WDHD1	cis	parietal	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55912600-55922000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr14:55913000-55919000	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr14:55913600-55921200	Weak transcription	HSMMtube	muscle
4	chr14:55913600-55925000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr14:55913800-55919200	Enhancers	Fetal Heart	heart
6	chr14:55913800-55920400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr14:55914000-55920600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr14:55914000-55920600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr14:55914000-55921000	Weak transcription	Brain Anterior Caudate	brain
10	chr14:55915000-55918600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr14:55915200-55918600	Weak transcription	Fetal Stomach	stomach
12	chr14:55915200-55920600	Weak transcription	Duodenum Mucosa	Duodenum
13	chr14:55915400-55919000	Enhancers	NHEK	skin
14	chr14:55915400-55920600	Weak transcription	Colon Smooth Muscle	Colon
15	chr14:55915600-55921000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr14:55915800-55920800	Weak transcription	Fetal Brain Female	brain
17	chr14:55916600-55918800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr14:55916600-55919000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr14:55916600-55920600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr14:55916800-55918800	Enhancers	Stomach Mucosa	stomach
21	chr14:55916800-55919000	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr14:55917000-55921000	Enhancers	HUVEC	blood vessel
23	chr14:55917000-55921400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr14:55917200-55918600	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr14:55917400-55918400	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr14:55917400-55918600	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr14:55917400-55918600	Enhancers	Brain Hippocampus Middle	brain
28	chr14:55917400-55918800	Enhancers	Primary hematopoietic stem cells	blood
29	chr14:55917400-55921000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr14:55917400-55921400	Weak transcription	GM12878-XiMat	blood
31	chr14:55917600-55918400	Enhancers	Monocytes-CD14+_RO01746	blood
32	chr14:55917600-55918600	Enhancers	HMEC	breast
33	chr14:55917600-55918800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr14:55917600-55918800	Enhancers	Pancreas	Pancrea
35	chr14:55917600-55918800	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr14:55917600-55919000	Enhancers	Esophagus	oesophagus
37	chr14:55917600-55919000	Enhancers	A549	lung
38	chr14:55917800-55919000	Enhancers	Hela-S3	cervix
39	chr14:55917800-55921000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr14:55918000-55918600	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr14:55918000-55918600	Enhancers	Small Intestine	intestine
42	chr14:55918000-55918800	Enhancers	Adipose Nuclei	Adipose
43	chr14:55918000-55918800	Enhancers	Right Atrium	heart
44	chr14:55918000-55919000	Enhancers	Muscle Satellite Cultured Cells	--
45	chr14:55918000-55919200	Enhancers	NHLF	lung
46	chr14:55918200-55918600	Enhancers	Ovary	ovary
47	chr14:55918200-55918600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
48	chr14:55918200-55918800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr14:55918200-55918800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr14:55918200-55918800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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