Variant report

Variant	rs363096
Chromosome Location	chr4:3180021-3180022
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	chr4:3116172..3119060-chr4:3178746..3180819,2	K562	blood:

Variant related genes	Relation type
ENSG00000197386	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10015979	0.89[GIH][hapmap]
rs110501	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs16843804	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs16843836	0.83[ASN][1000 genomes]
rs17780797	0.83[ASN][1000 genomes]
rs1891701	0.91[ASN][1000 genomes]
rs2024115	1.00[CHB][hapmap];0.80[CHD][hapmap];0.80[JPT][hapmap]
rs2071655	1.00[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs2071671	0.94[JPT][hapmap]
rs2071704	0.80[JPT][hapmap]
rs2157090	0.81[JPT][hapmap]
rs2269477	0.93[ASN][1000 genomes]
rs2269499	0.80[JPT][hapmap]
rs2285086	1.00[CHB][hapmap];0.80[CHD][hapmap];0.80[JPT][hapmap]
rs2298967	0.94[ASN][1000 genomes]
rs2298971	0.90[ASN][1000 genomes]
rs2530601	0.81[JPT][hapmap]
rs2798221	0.90[JPT][hapmap]
rs28403215	0.89[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs3095077	0.90[JPT][hapmap]
rs3121419	0.85[JPT][hapmap]
rs362271	0.80[JPT][hapmap]
rs362272	0.80[JPT][hapmap]
rs362273	0.95[JPT][hapmap]
rs362275	0.86[ASN][1000 genomes]
rs362296	0.84[JPT][hapmap]
rs362306	0.90[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap]
rs362331	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs362336	0.86[ASN][1000 genomes]
rs363063	0.93[ASN][1000 genomes]
rs363064	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs363066	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs363088	0.89[ASN][1000 genomes]
rs363092	0.90[ASN][1000 genomes]
rs363099	0.88[ASN][1000 genomes]
rs3755883	0.85[ASN][1000 genomes]
rs3856973	0.95[CHB][hapmap]
rs4690011	0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4690072	1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs4690073	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4690075	0.97[ASN][1000 genomes]
rs55962025	0.84[ASN][1000 genomes]
rs59613878	0.94[ASN][1000 genomes]
rs60197694	0.93[ASN][1000 genomes]
rs61792530	0.93[ASN][1000 genomes]
rs6446722	0.82[ASN][1000 genomes]
rs6446723	0.95[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs6446727	0.81[JPT][hapmap]
rs6446731	0.81[JPT][hapmap]
rs66684864	0.92[ASN][1000 genomes]
rs6844859	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6855981	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs73193303	0.93[ASN][1000 genomes]
rs7659144	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs7661630	0.81[JPT][hapmap]
rs7685686	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7691627	0.94[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs82332	0.85[ASN][1000 genomes]
rs82333	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs82334	0.85[ASN][1000 genomes]
rs916171	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs9996868	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv461163	chr4:2906285-3234980	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv593437	chr4:2906285-3234980	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
5	nsv461164	chr4:3149016-3215835	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
6	nsv593439	chr4:3149016-3215835	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
7	nsv998290	chr4:3176454-3355758	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs363096	TMEM175	cis	cerebellum	SCAN
rs363096	TMEM128	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3114600-3292400	Weak transcription	Right Atrium	heart
2	chr4:3145800-3239200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:3162600-3182200	Weak transcription	Small Intestine	intestine
4	chr4:3163000-3182000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr4:3167800-3203400	Strong transcription	Primary B cells from peripheral blood	blood
6	chr4:3168000-3180800	Strong transcription	Fetal Stomach	stomach
7	chr4:3168000-3182600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr4:3168000-3191800	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr4:3168000-3192600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr4:3168000-3197600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr4:3168000-3202800	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr4:3168000-3203000	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr4:3170000-3208800	Weak transcription	Stomach Mucosa	stomach
14	chr4:3170200-3181200	Weak transcription	K562	blood
15	chr4:3170200-3185000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr4:3170600-3182200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr4:3171200-3186600	Strong transcription	GM12878-XiMat	blood
18	chr4:3171200-3197600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr4:3171400-3187200	Strong transcription	Primary B cells from cord blood	blood
20	chr4:3171400-3192800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr4:3171600-3192800	Strong transcription	Primary T cells from cord blood	blood
22	chr4:3171600-3193600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr4:3171800-3180800	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr4:3172000-3192000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr4:3172000-3202800	Strong transcription	Duodenum Mucosa	Duodenum
26	chr4:3172200-3180400	Strong transcription	Liver	Liver
27	chr4:3172200-3193000	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr4:3172200-3195400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr4:3172400-3199800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:3172400-3238800	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr4:3172600-3192400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr4:3172800-3202800	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr4:3173000-3181200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr4:3173000-3192600	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr4:3173000-3193000	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr4:3173200-3182600	Strong transcription	Dnd41	blood
37	chr4:3173400-3180800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr4:3173400-3188800	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr4:3173600-3182400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr4:3173600-3182400	Strong transcription	NH-A	brain
41	chr4:3173600-3182400	Strong transcription	Osteobl	bone
42	chr4:3173600-3186800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr4:3173600-3187000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr4:3173600-3188000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr4:3173600-3192800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr4:3173600-3192800	Strong transcription	Placenta	Placenta
47	chr4:3173600-3193000	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr4:3173600-3200000	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr4:3173800-3192800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr4:3173800-3192800	Strong transcription	Fetal Thymus	thymus

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