Variant report

Variant	rs4975194
Chromosome Location	chr4:129982377-129982378
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	chr4:129979538..129981345-chr4:129981662..129983621,2	MCF-7	breast:
2	chr4:129977804..129979705-chr4:129980328..129983022,2	K562	blood:

Extended variants
information (count: 72 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10002332	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1030831	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1037147	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12171333	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13109003	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13130762	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1374491	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1596963	0.87[ASN][1000 genomes]
rs1699379	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1699380	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1699384	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1699385	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1699387	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1699388	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1699389	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1699391	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1699393	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1699394	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1709419	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1756012	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1757924	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1757925	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1757927	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1757928	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1757930	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1757935	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1757936	0.88[AMR][1000 genomes]
rs1854773	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1854774	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs189235	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2034498	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2198042	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2597836	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2655310	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs280603	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs280604	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3099899	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3105369	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3113489	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3113490	0.88[AMR][1000 genomes]
rs337263	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs337270	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs337275	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs337277	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs337278	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35006492	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs389376	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs390260	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs391396	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs395864	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs426521	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4394010	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs445294	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4466058	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs474667	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs474794	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs487233	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs487501	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4975193	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs517659	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57501568	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs576492	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58689608	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6534707	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66921209	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7655841	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7671508	0.88[AMR][1000 genomes]
rs789982	0.88[AMR][1000 genomes]

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	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	nsv522694	chr4:129862073-129994690	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4975194	C4orf33	cis	multi-tissue	Pritchard
rs4975194	SCLT1	Cis_1M	lymphoblastoid	RTeQTL
rs4975194	C4orf33	Cis_1M	lymphoblastoid	RTeQTL
rs4975194	C4orf33	cis	Whole Blood	GTEx
rs4975194	C4orf33	cis	Artery Tibial	GTEx
rs4975194	PHF17	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129977200-130000600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:129979400-129983800	Weak transcription	NH-A	brain
3	chr4:129980000-129983000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:129980000-129986000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
5	chr4:129980200-129985200	ZNF genes & repeats	Adipose Nuclei	Adipose
6	chr4:129980200-129985400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
7	chr4:129980200-129986200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr4:129980400-129985000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
9	chr4:129980400-129985600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr4:129980800-129984200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr4:129980800-129985000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
12	chr4:129981200-129982600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr4:129981200-129987200	ZNF genes & repeats	Dnd41	blood
14	chr4:129981400-129985000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
15	chr4:129981400-129985200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr4:129981400-129985200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
17	chr4:129981400-129985200	ZNF genes & repeats	Fetal Muscle Leg	muscle
18	chr4:129981400-129987000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr4:129981600-129983400	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr4:129981600-129983400	ZNF genes & repeats	Aorta	Aorta
21	chr4:129981600-129983400	ZNF genes & repeats	Gastric	stomach
22	chr4:129981600-129985200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr4:129981600-129985200	ZNF genes & repeats	Primary T cells from cord blood	blood
24	chr4:129981600-129985200	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
25	chr4:129981600-129985200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr4:129981600-129985200	ZNF genes & repeats	Liver	Liver
27	chr4:129981600-129985200	ZNF genes & repeats	Fetal Brain Female	brain
28	chr4:129981600-129985200	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
29	chr4:129981800-129983400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr4:129981800-129983400	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
31	chr4:129981800-129983400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr4:129981800-129983400	ZNF genes & repeats	Fetal Stomach	stomach
33	chr4:129981800-129983600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
34	chr4:129981800-129983600	ZNF genes & repeats	Thymus	Thymus
35	chr4:129981800-129985000	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
36	chr4:129981800-129985200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr4:129981800-129985200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
38	chr4:129981800-129985200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
39	chr4:129981800-129985200	ZNF genes & repeats	Fetal Intestine Small	intestine
40	chr4:129981800-129985200	ZNF genes & repeats	A549	lung
41	chr4:129981800-129985400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr4:129982000-129982400	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr4:129982000-129982400	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr4:129982000-129983400	ZNF genes & repeats	Left Ventricle	heart
45	chr4:129982000-129983400	ZNF genes & repeats	Pancreas	Pancrea
46	chr4:129982000-129983600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr4:129982000-129983600	ZNF genes & repeats	Ovary	ovary
48	chr4:129982000-129985000	ZNF genes & repeats	Brain Hippocampus Middle	brain
49	chr4:129982000-129985200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
50	chr4:129982200-129983000	Active TSS	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links