Variant report

Variant	rs2655310
Chromosome Location	chr4:130017919-130017920
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F4	chr4:130017781-130017959	MCF10A-Er-Src	breast:	n/a	n/a
2	MXI1	chr4:130016860-130018171	SK-N-SH	brain:	n/a	n/a
3	TBL1XR1	chr4:130017697-130017923	GM12878	blood:	n/a	n/a
4	IRF1	chr4:130016415-130017935	K562	blood:	n/a	chr4:130017752-130017761 chr4:130017569-130017583 chr4:130017543-130017557 chr4:130017565-130017579 chr4:130017569-130017579 chr4:130017750-130017760 chr4:130017561-130017581
5	MAFK	chr4:130017103-130017999	K562	blood:	n/a	n/a
6	ARID3A	chr4:130015591-130017978	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:130017343..130020226-chr4:130031173..130032927,2	K562	blood:

Variant related genes	Relation type
SCLT1	TF binding region

Extended variants
information (count: 79 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10002332	1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[EUR][1000 genomes]
rs10032000	0.93[CEU][hapmap]
rs1030831	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1037147	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11934740	0.81[TSI][hapmap]
rs12171333	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[EUR][1000 genomes]
rs13109003	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13130762	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1374491	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1668289	0.93[CEU][hapmap]
rs1699379	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1699380	0.94[ASW][hapmap];0.93[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1699384	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1699385	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1699387	0.94[ASW][hapmap];0.93[CEU][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1699388	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1699389	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1699391	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1699393	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1699394	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17014265	0.88[CHB][hapmap]
rs1709419	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1756012	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1757924	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1757925	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1757927	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1757928	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.95[LWK][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1757930	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1757935	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1757936	0.81[TSI][hapmap]
rs1854773	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1854774	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes]
rs189235	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2034498	0.90[EUR][1000 genomes]
rs2083634	1.00[CEU][hapmap]
rs2198042	1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[EUR][1000 genomes]
rs2597836	0.88[EUR][1000 genomes]
rs280603	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs280604	1.00[CEU][hapmap];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3099899	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3105369	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3113407	0.93[CEU][hapmap]
rs3113489	0.93[CEU][hapmap];0.88[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.81[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs318536	0.93[CEU][hapmap]
rs318543	0.93[CEU][hapmap]
rs318552	0.93[CEU][hapmap]
rs337263	0.93[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs337270	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs337275	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs337277	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]
rs337278	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35006492	0.93[EUR][1000 genomes]
rs389376	0.93[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs390260	0.94[ASW][hapmap];0.93[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs391396	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs395864	0.93[CEU][hapmap];0.88[CHB][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs426521	0.88[ASW][hapmap];0.93[CEU][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4394010	0.93[EUR][1000 genomes]
rs445294	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4466058	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs474667	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs474794	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs487233	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs487501	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4975193	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.82[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4975194	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs517659	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57501568	0.94[EUR][1000 genomes]
rs576492	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58689608	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6534707	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs66921209	0.91[EUR][1000 genomes]
rs6824219	0.80[TSI][hapmap]
rs7655841	1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs7671508	0.81[TSI][hapmap]
rs789982	0.81[TSI][hapmap]

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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2655310	SCLT1	cis	cerebellum	SCAN
rs2655310	PHF17	Cis_1M	lymphoblastoid	RTeQTL
rs2655310	C4orf33	cis	cerebellum	SCAN
rs2655310	ZNF226	trans	cerebellum	SCAN
rs2655310	C4orf33	cis	Artery Tibial	GTEx
rs2655310	C4orf33	cis	parietal	SCAN
rs2655310	C4orf33	cis	lymphoblastoid	seeQTL
rs2655310	SCLT1	Cis_1M	lymphoblastoid	RTeQTL
rs2655310	C4orf33	cis	Adipose Subcutaneous	GTEx
rs2655310	C4orf33	cis	Whole Blood	GTEx
rs2655310	C4orf33	cis	multi-tissue	Pritchard
rs2655310	C4orf33	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:130012800-130018600	Active TSS	K562	blood
2	chr4:130016800-130018000	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr4:130017000-130018000	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr4:130017000-130018000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:130017000-130018000	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr4:130017000-130018000	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr4:130017000-130018000	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr4:130017000-130018000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr4:130017000-130018000	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr4:130017000-130018000	Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr4:130017000-130018000	Active TSS	Muscle Satellite Cultured Cells	--
12	chr4:130017000-130018000	Active TSS	Liver	Liver
13	chr4:130017000-130018000	Active TSS	Brain Anterior Caudate	brain
14	chr4:130017000-130018000	Active TSS	Brain Cingulate Gyrus	brain
15	chr4:130017000-130018000	Active TSS	Brain Inferior Temporal Lobe	brain
16	chr4:130017000-130018000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
17	chr4:130017000-130018000	Active TSS	Fetal Intestine Large	intestine
18	chr4:130017000-130018000	Active TSS	Fetal Kidney	kidney
19	chr4:130017000-130018000	Active TSS	Fetal Lung	lung
20	chr4:130017000-130018000	Active TSS	Fetal Muscle Leg	muscle
21	chr4:130017000-130018000	Active TSS	Fetal Thymus	thymus
22	chr4:130017000-130018000	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr4:130017000-130018000	Active TSS	Rectal Smooth Muscle	rectum
24	chr4:130017000-130018000	Active TSS	Right Atrium	heart
25	chr4:130017000-130018000	Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr4:130017000-130018000	Active TSS	Stomach Smooth Muscle	stomach
27	chr4:130017000-130018000	Active TSS	A549	lung
28	chr4:130017000-130018000	Active TSS	HMEC	breast
29	chr4:130017000-130018000	Active TSS	NHDF-Ad	bronchial
30	chr4:130017000-130018000	Active TSS	NHEK	skin
31	chr4:130017000-130018000	Active TSS	NHLF	lung
32	chr4:130017000-130018200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr4:130017000-130018200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr4:130017000-130018200	Active TSS	Duodenum Mucosa	Duodenum
35	chr4:130017000-130018200	Active TSS	Rectal Mucosa Donor 31	rectum
36	chr4:130017000-130018200	Active TSS	HepG2	liver
37	chr4:130017000-130018600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr4:130017200-130018000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
39	chr4:130017200-130018000	Active TSS	H1 Cell Line	embryonic stem cell
40	chr4:130017200-130018000	Active TSS	HUES64 Cell Line	embryonic stem cell
41	chr4:130017200-130018000	Active TSS	iPS-15b Cell Line	embryonic stem cell
42	chr4:130017200-130018000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr4:130017200-130018000	Active TSS	Primary T cells from cord blood	blood
44	chr4:130017200-130018000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
45	chr4:130017200-130018000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
46	chr4:130017200-130018000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
47	chr4:130017200-130018000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr4:130017200-130018000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr4:130017200-130018000	Active TSS	Adipose Nuclei	Adipose
50	chr4:130017200-130018000	Active TSS	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links