Variant report

Variant	rs337277
Chromosome Location	chr4:130030652-130030653
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	chr4:130028612..130032885-chr4:130034533..130038076,4	K562	blood:
2	chr4:130016811..130018754-chr4:130029159..130031907,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151470	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10002332	0.93[CEU][hapmap];0.92[EUR][1000 genomes]
rs10032000	0.87[CEU][hapmap]
rs1030831	0.94[ASW][hapmap];0.93[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1037147	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12171333	0.93[CEU][hapmap];0.92[EUR][1000 genomes]
rs13109003	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13130762	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1374491	0.93[CEU][hapmap];0.88[CHB][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1699379	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1699380	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1699384	0.93[CEU][hapmap];0.88[CHB][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1699385	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1699387	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1699388	0.93[CEU][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1699389	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1699391	0.93[CEU][hapmap];0.88[CHB][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1699393	0.93[CEU][hapmap];0.88[CHB][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1699394	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17014265	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs1709419	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1756012	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1757924	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1757925	0.88[ASW][hapmap];0.93[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1757927	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1757928	0.87[CEU][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1757930	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1757935	0.93[CEU][hapmap];0.88[CHB][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1854773	0.93[CEU][hapmap];0.88[CHB][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1854774	0.93[CEU][hapmap];0.88[CHB][hapmap];0.86[YRI][hapmap];0.83[EUR][1000 genomes]
rs189235	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2034498	0.90[EUR][1000 genomes]
rs2083634	0.93[CEU][hapmap]
rs2198042	0.93[CEU][hapmap];0.94[EUR][1000 genomes]
rs2597836	0.87[EUR][1000 genomes]
rs2655310	0.94[ASW][hapmap];0.93[CEU][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs280603	0.93[CEU][hapmap];0.94[EUR][1000 genomes]
rs280604	0.93[CEU][hapmap];0.92[EUR][1000 genomes]
rs3099899	0.92[CEU][hapmap];0.88[CHB][hapmap];0.94[EUR][1000 genomes]
rs3105369	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3113489	0.87[CEU][hapmap];0.83[LWK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs318536	0.93[CEU][hapmap]
rs318543	0.87[CEU][hapmap]
rs318552	0.87[CEU][hapmap]
rs337263	0.83[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.89[LWK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs337270	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs337275	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs337278	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35006492	0.92[EUR][1000 genomes]
rs389376	0.83[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.89[LWK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs390260	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs391396	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs395864	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs426521	0.94[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4394010	0.92[EUR][1000 genomes]
rs445294	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4466058	0.93[CEU][hapmap];0.88[CHB][hapmap];0.94[EUR][1000 genomes]
rs474667	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs474794	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs487233	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs487501	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4975193	0.82[ASW][hapmap];0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4975194	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs517659	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57501568	0.93[EUR][1000 genomes]
rs576492	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58689608	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6534707	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs66921209	0.90[EUR][1000 genomes]
rs7655841	0.93[CEU][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv534538	chr4:129799138-130431688	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv879931	chr4:129939775-130178102	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs337277	ZNF226	trans	cerebellum	SCAN
rs337277	C4orf33	Cis_1M	lymphoblastoid	RTeQTL
rs337277	C4orf33	cis	parietal	SCAN
rs337277	C4orf33	cis	cerebellum	SCAN
rs337277	C4orf33	cis	Artery Tibial	GTEx
rs337277	C4orf33	cis	multi-tissue	Pritchard
rs337277	C4orf33	cis	Whole Blood	GTEx
rs337277	SCLT1	cis	cerebellum	SCAN
rs337277	C4orf33	cis	Lymphoblastoid	GTEx
rs337277	C4orf33	cis	lymphoblastoid	seeQTL
rs337277	C4orf33	cis	Adipose Subcutaneous	GTEx
rs337277	PHF17	Cis_1M	lymphoblastoid	RTeQTL
rs337277	SCLT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:130017600-130031400	Weak transcription	Pancreas	Pancrea
2	chr4:130017600-130031400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:130017600-130040400	Weak transcription	Lung	lung
4	chr4:130017800-130030800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr4:130017800-130031400	Weak transcription	Aorta	Aorta
6	chr4:130017800-130031400	Weak transcription	Left Ventricle	heart
7	chr4:130017800-130031400	Weak transcription	Ovary	ovary
8	chr4:130017800-130031400	Weak transcription	Right Ventricle	heart
9	chr4:130017800-130031600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr4:130017800-130032600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr4:130017800-130032800	Weak transcription	Colon Smooth Muscle	Colon
12	chr4:130017800-130033400	Weak transcription	Brain Hippocampus Middle	brain
13	chr4:130017800-130033400	Weak transcription	Thymus	Thymus
14	chr4:130017800-130034200	Weak transcription	Colonic Mucosa	Colon
15	chr4:130018000-130031000	Weak transcription	Fetal Thymus	thymus
16	chr4:130018000-130031400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr4:130018000-130031400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr4:130018000-130031400	Weak transcription	Fetal Stomach	stomach
19	chr4:130018000-130032400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr4:130018000-130033000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr4:130018000-130033200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr4:130018000-130033400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr4:130018000-130034000	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr4:130018000-130038000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr4:130018200-130031800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr4:130018200-130032400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr4:130018600-130032000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr4:130018800-130033800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr4:130023600-130033400	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr4:130025000-130032000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr4:130025200-130033200	Weak transcription	Fetal Lung	lung
32	chr4:130025400-130032200	Weak transcription	Fetal Brain Male	brain
33	chr4:130025800-130035000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr4:130026400-130030800	Weak transcription	Primary hematopoietic stem cells	blood
35	chr4:130026400-130031000	Weak transcription	Rectal Smooth Muscle	rectum
36	chr4:130026800-130032200	Weak transcription	Placenta	Placenta
37	chr4:130027800-130031600	Weak transcription	Stomach Smooth Muscle	stomach
38	chr4:130028400-130033600	Weak transcription	Fetal Brain Female	brain
39	chr4:130028800-130032200	Weak transcription	NHDF-Ad	bronchial
40	chr4:130028800-130032400	Weak transcription	Brain Anterior Caudate	brain
41	chr4:130028800-130036600	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr4:130029200-130032600	Weak transcription	HSMMtube	muscle
43	chr4:130029200-130040000	Weak transcription	Esophagus	oesophagus
44	chr4:130029400-130035400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr4:130029400-130041200	Weak transcription	Spleen	Spleen
46	chr4:130029600-130038600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr4:130029800-130033000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr4:130030200-130031400	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr4:130030200-130031800	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr4:130030200-130031800	Strong transcription	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links