Variant report

Variant	rs4975270
Chromosome Location	chr4:129757215-129757216
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:129731063..129734279-chr4:129754821..129757246,3	K562	blood:
2	chr4:129739255..129743318-chr4:129756229..129760124,4	K562	blood:
3	chr4:129736160..129738692-chr4:129755365..129757627,2	K562	blood:

Variant related genes	Relation type
ENSG00000077684	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10008927	0.88[JPT][hapmap]
rs10017436	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10518539	0.83[LWK][hapmap];0.85[YRI][hapmap]
rs11098987	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11724119	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.88[JPT][hapmap];0.87[TSI][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11731189	0.91[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.83[TSI][hapmap]
rs1425618	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1648062	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs167618	0.87[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17013778	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1993035	1.00[YRI][hapmap]
rs2016294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs318504	0.96[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs318505	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs318555	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs318556	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4423892	0.85[YRI][hapmap]
rs4975263	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4975264	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4975266	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.89[TSI][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4975268	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4975269	0.82[JPT][hapmap]
rs55829553	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62317868	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6832138	1.00[YRI][hapmap]
rs6833391	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6835359	0.85[YRI][hapmap]
rs6844446	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6857659	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1020801	chr4:129658178-129778086	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv537248	chr4:129658178-129778086	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv517249	chr4:129738328-129927804	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4975270	SCLT1	cis	cerebellum	SCAN
rs4975270	PHF17	Cis_1M	lymphoblastoid	RTeQTL
rs4975270	LOC132321	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129746600-129761800	Strong transcription	Dnd41	blood
2	chr4:129746800-129770200	Weak transcription	HMEC	breast
3	chr4:129747000-129766600	Weak transcription	NHEK	skin
4	chr4:129747400-129761600	Weak transcription	Placenta	Placenta
5	chr4:129748000-129761600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr4:129752400-129758000	Strong transcription	Primary T cells from cord blood	blood
7	chr4:129752400-129758600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr4:129752400-129763800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr4:129752600-129761800	Strong transcription	Fetal Thymus	thymus
10	chr4:129752800-129758200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr4:129752800-129758200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr4:129752800-129760600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr4:129753000-129757400	Strong transcription	Primary B cells from cord blood	blood
14	chr4:129753000-129758000	Strong transcription	Thymus	Thymus
15	chr4:129753000-129758600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr4:129753000-129761000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr4:129753000-129766200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr4:129753200-129759000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr4:129753200-129759200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr4:129753200-129759200	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr4:129753200-129763800	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr4:129753200-129767600	Weak transcription	Colonic Mucosa	Colon
23	chr4:129753400-129764000	Weak transcription	Fetal Brain Female	brain
24	chr4:129753400-129766000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr4:129753400-129767600	Weak transcription	Fetal Brain Male	brain
26	chr4:129753600-129757400	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr4:129753600-129758800	Strong transcription	Osteobl	bone
28	chr4:129753600-129767600	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr4:129753600-129798600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:129753800-129759800	Strong transcription	Primary B cells from peripheral blood	blood
31	chr4:129753800-129770400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr4:129753800-129795000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr4:129754000-129758600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr4:129754000-129759400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr4:129754000-129761600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr4:129754200-129758400	Strong transcription	A549	lung
37	chr4:129754200-129758600	Weak transcription	K562	blood
38	chr4:129754200-129758800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
39	chr4:129754400-129758600	Strong transcription	GM12878-XiMat	blood
40	chr4:129754400-129770600	Weak transcription	Fetal Kidney	kidney
41	chr4:129755000-129763000	Enhancers	Fetal Heart	heart
42	chr4:129755400-129757800	Genic enhancers	HUES64 Cell Line	embryonic stem cell
43	chr4:129755400-129761000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
44	chr4:129755400-129764800	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr4:129755600-129758200	Weak transcription	NHDF-Ad	bronchial
46	chr4:129755800-129759000	Enhancers	Stomach Mucosa	stomach
47	chr4:129756000-129757400	Genic enhancers	Fetal Muscle Leg	muscle
48	chr4:129756000-129758200	Strong transcription	NH-A	brain
49	chr4:129756000-129758400	Strong transcription	Fetal Intestine Large	intestine
50	chr4:129756200-129757400	Genic enhancers	Primary T helper cells PMA-I stimulated	--

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