Variant report

Variant	rs3795396
Chromosome Location	chr1:153635425-153635426
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:153579256..153583611-chr1:153630358..153635573,4	MCF-7	breast:
2	chr1:153635410..153637927-chr1:153928123..153932423,3	K562	blood:
3	chr1:153516744..153518266-chr1:153633829..153635751,2	MCF-7	breast:
4	chr1:153634344..153636608-chr1:153747089..153749538,2	K562	blood:

Variant related genes	Relation type
ENSG00000196154	Chromatin interaction
ENSG00000188643	Chromatin interaction
ENSG00000160741	Chromatin interaction
ENSG00000143554	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1046381	0.95[EUR][1000 genomes]
rs10797056	0.92[CEU][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10797090	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10797096	0.95[CHB][hapmap];0.83[CHD][hapmap];0.85[ASN][1000 genomes]
rs10908746	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10908848	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs11265625	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs11265633	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1128894	0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11497739	0.82[TSI][hapmap]
rs11548104	0.82[TSI][hapmap]
rs11580122	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11588347	0.82[ASN][1000 genomes]
rs12139953	0.85[ASN][1000 genomes]
rs12564925	0.92[CEU][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12730186	0.80[ASN][1000 genomes]
rs1810836	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1888115	0.92[CEU][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2274739	0.92[CEU][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2274740	0.92[CEU][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28379831	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28380060	0.92[CEU][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28416529	0.85[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs28510471	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28580554	0.92[CEU][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28613361	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28700217	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3790411	0.90[CHD][hapmap];0.88[GIH][hapmap];0.80[MEX][hapmap];0.80[TSI][hapmap]
rs3790412	0.92[CEU][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3806233	0.83[CHD][hapmap]
rs3806234	0.90[CHB][hapmap];0.93[CHD][hapmap];0.85[ASN][1000 genomes]
rs3818632	0.92[CEU][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3828031	0.92[CEU][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3862047	0.95[CHB][hapmap];0.90[CHD][hapmap];0.90[ASN][1000 genomes]
rs4351684	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4515830	0.94[CHB][hapmap]
rs4845557	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4845558	0.84[EUR][1000 genomes]
rs4845560	0.87[EUR][1000 genomes]
rs4845563	0.85[CHB][hapmap];0.93[CHD][hapmap];0.85[ASN][1000 genomes]
rs4845564	0.82[ASN][1000 genomes]
rs55772653	0.85[ASN][1000 genomes]
rs6427640	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66721814	0.85[ASN][1000 genomes]
rs6674929	0.95[CHB][hapmap];0.83[CHD][hapmap];0.82[ASN][1000 genomes]
rs7345	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7541193	0.80[MEX][hapmap]
rs7934	0.92[CEU][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs913860	0.92[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs913861	1.00[CEU][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9330299	0.80[MEX][hapmap];0.82[TSI][hapmap]
rs9330301	0.80[MEX][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs9661993	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9662664	0.90[CHB][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv547928	chr1:153612133-153714252	Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	esv2830411	chr1:153613393-153725007	Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
5	nsv1067771	chr1:153613593-153724866	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	nsv530052	chr1:153613593-153724866	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
7	nsv1005818	chr1:153613597-153724980	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	nsv535173	chr1:153613597-153724980	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
9	nsv1007835	chr1:153613597-153729959	Genic enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
10	nsv535174	chr1:153613597-153729959	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
11	nsv1011897	chr1:153613597-153836703	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking 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	70 gene(s)	inside rSNPs	diseases
12	nsv464028	chr1:153622220-153723037	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
13	nsv547929	chr1:153622220-153723037	Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
14	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
15	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
16	nsv1001312	chr1:153622834-153724867	Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
17	nsv535176	chr1:153622834-153724867	Active TSS Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs3795396	S100A16	cis	parietal	SCAN
rs3795396	S100A13	cis	Adipose Subcutaneous	GTEx
rs3795396	RP1-178F15.4	cis	Heart Left Ventricle	GTEx
rs3795396	SNAPIN	cis	lymphoblastoid	seeQTL
rs3795396	S100A13	cis	parietal	SCAN
rs3795396	S100A13	cis	lymphoblastoid	seeQTL
rs3795396	RP1-178F15.4	cis	Adipose Subcutaneous	GTEx
rs3795396	S100A10	cis	cerebellum	SCAN
rs3795396	S100A13	cis	Lymphoblastoid	GTEx
rs3795396	S100A13	Cis_1M	lymphoblastoid	RTeQTL
rs3795396	S100A2	cis	cerebellum	SCAN
rs3795396	S100A16	cis	cerebellum	SCAN
rs3795396	CHTOP	cis	Muscle Skeletal	GTEx
rs3795396	S100A13	cis	multi-tissue	Pritchard
rs3795396	SLC27A3	cis	cerebellum	SCAN
rs3795396	RP1-178F15.5	cis	Adipose Subcutaneous	GTEx
rs3795396	RP1-178F15.4	cis	Muscle Skeletal	GTEx
rs3795396	RP1-178F15.4	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153632000-153642200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:153632000-153642800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:153632400-153640800	Strong transcription	Fetal Muscle Leg	muscle
4	chr1:153632400-153641200	Strong transcription	Fetal Muscle Trunk	muscle
5	chr1:153632400-153641600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr1:153632400-153641800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
7	chr1:153632400-153642000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:153632400-153642400	Weak transcription	Right Atrium	heart
9	chr1:153632600-153635600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:153632600-153635600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:153632600-153640400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:153632600-153640800	Strong transcription	Brain Germinal Matrix	brain
13	chr1:153632600-153641200	Strong transcription	Placenta	Placenta
14	chr1:153632600-153641200	Strong transcription	Fetal Thymus	thymus
15	chr1:153632600-153641400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr1:153632600-153641400	Strong transcription	Brain Cingulate Gyrus	brain
17	chr1:153632600-153641600	Strong transcription	Lung	lung
18	chr1:153632600-153641800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:153632600-153641800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:153632600-153641800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:153632600-153641800	Strong transcription	Skeletal Muscle Male	skeletal muscle
22	chr1:153632600-153641800	Strong transcription	Stomach Smooth Muscle	stomach
23	chr1:153632600-153642200	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr1:153632600-153642200	Strong transcription	Fetal Stomach	stomach
25	chr1:153632800-153636200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr1:153632800-153641800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:153632800-153641800	Strong transcription	Fetal Intestine Large	intestine
28	chr1:153632800-153642000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:153632800-153642000	Strong transcription	Fetal Intestine Small	intestine
30	chr1:153633000-153642000	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr1:153633000-153642000	Strong transcription	Primary B cells from peripheral blood	blood
32	chr1:153633200-153635600	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr1:153633200-153640200	Strong transcription	Primary T cells from cord blood	blood
34	chr1:153633200-153640400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
35	chr1:153633200-153640400	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr1:153633200-153640800	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr1:153633200-153640800	Strong transcription	Primary B cells from cord blood	blood
38	chr1:153633200-153640800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr1:153633200-153640800	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr1:153633200-153640800	Strong transcription	Thymus	Thymus
41	chr1:153633200-153641000	Strong transcription	Rectal Smooth Muscle	rectum
42	chr1:153633200-153641200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr1:153633200-153641200	Strong transcription	Fetal Brain Female	brain
44	chr1:153633200-153641400	Strong transcription	Left Ventricle	heart
45	chr1:153633200-153641600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr1:153633200-153641600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr1:153633200-153641600	Strong transcription	Right Ventricle	heart
48	chr1:153633200-153641800	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr1:153633200-153641800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr1:153633200-153641800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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