Variant report

Variant	rs10001548
Chromosome Location	chr4:165879381-165879382
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	chr4:165868972..165872041-chr4:165876298..165879460,3	MCF-7	breast:
2	chr4:165874581..165877460-chr4:165878651..165880772,2	K562	blood:

Variant related genes	Relation type
ENSG00000236941	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10016502	0.89[ASN][1000 genomes]
rs10020142	0.88[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.85[ASN][1000 genomes]
rs10020204	0.88[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.89[ASN][1000 genomes]
rs10025595	0.85[ASN][1000 genomes]
rs10034083	0.84[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11100586	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11936657	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11941364	0.89[ASN][1000 genomes]
rs12501482	0.85[ASN][1000 genomes]
rs12505213	0.88[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap]
rs12510353	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12510406	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17584656	0.88[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap]
rs2280326	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs28475532	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28544252	0.88[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.81[MEX][hapmap]
rs28548593	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28581275	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28624277	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28631315	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28633542	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3196673	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4286486	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs4350966	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4359860	0.88[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap]
rs4380479	0.88[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs4396952	0.89[ASN][1000 genomes]
rs4511961	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56231925	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6536884	0.84[ASN][1000 genomes]
rs6536885	0.88[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap]
rs6814756	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6827270	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6828659	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6847301	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs6848637	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6856935	0.86[JPT][hapmap]
rs7654142	0.85[CHD][hapmap]
rs7663962	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs7680569	0.96[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019150	chr4:165505585-165907924	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1026152	chr4:165622244-166027447	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv537336	chr4:165622244-166027447	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Active 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	36 gene(s)	inside rSNPs	diseases
4	nsv1022210	chr4:165792630-166251612	Genic enhancers Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv537337	chr4:165792630-166251612	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	nsv880382	chr4:165793001-165964290	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
7	esv2757965	chr4:165801816-165976350	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	esv2759299	chr4:165801816-165976350	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv528686	chr4:165814359-165930168	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv967697	chr4:165843736-165889668	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv1015970	chr4:165852926-165973078	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv1021905	chr4:165852926-166212878	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
13	nsv830140	chr4:165855999-165956612	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
14	esv2760876	chr4:165861386-165893486	Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	esv20237	chr4:165861441-165883885	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
16	nsv10607	chr4:165861465-165886549	Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
17	esv3692850	chr4:165868229-165879381	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
18	esv2421831	chr4:165868229-165882293	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10001548	FAM218A	cis	Thyroid	GTEx

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:165877600-165879400	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr4:165877600-165879400	Active TSS	Brain Hippocampus Middle	brain
3	chr4:165877600-165879600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr4:165877600-165879600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr4:165877600-165879800	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr4:165877600-165880000	Active TSS	Brain Germinal Matrix	brain
7	chr4:165877600-165880200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr4:165877600-165880200	Active TSS	HSMM	muscle
9	chr4:165877600-165880400	Active TSS	HSMMtube	muscle
10	chr4:165877800-165879400	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr4:165877800-165879400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr4:165877800-165879400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr4:165877800-165879400	Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr4:165877800-165879400	Active TSS	Fetal Brain Male	brain
15	chr4:165877800-165879600	Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr4:165877800-165879800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr4:165877800-165879800	Active TSS	Brain Cingulate Gyrus	brain
18	chr4:165877800-165879800	Active TSS	Osteobl	bone
19	chr4:165877800-165880000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr4:165878000-165879400	Active TSS	Muscle Satellite Cultured Cells	--
21	chr4:165878000-165879800	Active TSS	NHEK	skin
22	chr4:165878200-165879800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr4:165878400-165879600	Active TSS	HMEC	breast
24	chr4:165878400-165879800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr4:165878600-165879400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr4:165878600-165879600	Active TSS	Skeletal Muscle Female	skeletal muscle
27	chr4:165878800-165879400	Flanking Active TSS	GM12878-XiMat	blood
28	chr4:165878800-165879600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr4:165878800-165879600	Flanking Active TSS	Fetal Brain Female	brain
30	chr4:165878800-165881200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr4:165878800-165881200	Weak transcription	Fetal Intestine Small	intestine
32	chr4:165878800-165884000	Weak transcription	Pancreas	Pancrea
33	chr4:165878800-165888600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr4:165878800-165888600	Weak transcription	Fetal Muscle Trunk	muscle
35	chr4:165878800-165891800	Weak transcription	Fetal Muscle Leg	muscle
36	chr4:165878800-165892000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr4:165878800-165893400	Weak transcription	Primary B cells from peripheral blood	blood
38	chr4:165878800-165893600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr4:165878800-165895000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr4:165878800-165895200	Weak transcription	Fetal Thymus	thymus
41	chr4:165878800-165897800	Weak transcription	Left Ventricle	heart
42	chr4:165878800-165898200	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr4:165879000-165879400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
44	chr4:165879000-165879400	Enhancers	Fetal Kidney	kidney
45	chr4:165879000-165879400	Enhancers	Stomach Smooth Muscle	stomach
46	chr4:165879000-165879800	Enhancers	Colon Smooth Muscle	Colon
47	chr4:165879000-165880200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr4:165879000-165880200	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr4:165879000-165880800	Weak transcription	A549	lung
50	chr4:165879000-165897600	Weak transcription	Fetal Lung	lung

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