Variant report

Variant	rs11729258
Chromosome Location	chr4:76647710-76647711
allele	G/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	MAFF	chr4:76647581-76647967	K562	blood:	n/a	n/a
2	MAFK	chr4:76647648-76647987	K562	blood:	n/a	chr4:76647796-76647807 chr4:76647794-76647808 chr4:76647795-76647806 chr4:76647796-76647807 chr4:76647795-76647806

No.	Distal block	Cell Line	Cell type
1	chr4:76646646..76648324-chr4:76652983..76654497,2	K562	blood:
2	chr4:76596286..76601002-chr4:76645864..76652581,23	K562	blood:
3	chr4:76574170..76576945-chr4:76646198..76647793,2	K562	blood:
4	chr4:76596470..76600480-chr4:76647707..76650691,10	MCF-7	breast:
5	chr4:76595601..76600505-chr4:76645864..76652704,29	K562	blood:
6	chr4:76584918..76589893-chr4:76647342..76651400,4	K562	blood:
7	chr4:76595422..76600363-chr4:76647674..76651574,9	MCF-7	breast:

Variant related genes	Relation type
USO1	TF binding region
ENSG00000201644	Chromatin interaction
ENSG00000138757	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10009902	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10010519	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10014281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10025315	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10028884	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10029110	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11097069	0.81[EUR][1000 genomes]
rs11097070	1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11736474	0.81[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13116639	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13118426	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13133699	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13137468	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13138717	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1464071	0.81[CEU][hapmap]
rs1546539	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1548175	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1553984	1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1553986	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1967495	0.82[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1967496	0.82[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs226416	0.91[CEU][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2280095	1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2869174	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs324682	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs324683	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs324685	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs324689	0.91[CEU][hapmap];0.82[CHB][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs324692	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs324695	0.91[CEU][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs324707	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs324708	0.91[CEU][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs324711	0.91[CEU][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs324715	0.91[CEU][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs324716	0.91[CEU][hapmap];0.82[CHB][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs324717	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs324718	0.91[CEU][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs324721	0.91[CEU][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs324724	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs324725	0.91[CEU][hapmap];0.82[CHB][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs324737	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3796473	0.81[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3796485	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3796488	0.81[CEU][hapmap]
rs3853183	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3853184	0.91[CEU][hapmap];0.82[CHB][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3942252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4349625	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs436611	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs443952	0.91[CEU][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4859403	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4859542	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4859543	0.81[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4859544	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4859545	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4859546	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4859547	0.81[CEU][hapmap];0.82[CHB][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4859548	0.82[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4859550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5020591	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6419115	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6531778	0.81[CEU][hapmap]
rs6531841	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6531866	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6531867	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6531868	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6531889	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6531902	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6531903	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6826858	0.81[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6827809	1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6832912	0.81[CEU][hapmap]
rs6835702	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6835819	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6842216	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6855321	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6858741	0.84[AMR][1000 genomes]
rs72651313	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7356270	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7356310	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7657871	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7659408	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7662940	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7672378	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7674063	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7674328	1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7677150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7685459	1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7691385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7691765	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7696241	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7698393	0.85[EUR][1000 genomes]
rs9942164	0.85[AMR][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	esv3353539	chr4:76530136-76993859	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised 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	51 gene(s)	inside rSNPs	diseases
2	nsv1003516	chr4:76597112-76729576	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv537143	chr4:76597112-76729576	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76624400-76647800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr4:76631000-76648800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:76631600-76648000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr4:76633600-76648200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr4:76633800-76648000	Weak transcription	Fetal Kidney	kidney
6	chr4:76634000-76647800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr4:76634000-76647800	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr4:76635400-76648200	Weak transcription	Primary B cells from cord blood	blood
9	chr4:76636400-76648600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr4:76640400-76648200	Weak transcription	Stomach Mucosa	stomach
11	chr4:76640800-76648200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr4:76640800-76648200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr4:76640800-76648400	Weak transcription	Placenta	Placenta
14	chr4:76640800-76648400	Weak transcription	Right Atrium	heart
15	chr4:76640800-76649200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr4:76640800-76649400	Weak transcription	Lung	lung
17	chr4:76641000-76647800	Weak transcription	Brain Germinal Matrix	brain
18	chr4:76641000-76648000	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr4:76641000-76648200	Weak transcription	Brain Anterior Caudate	brain
20	chr4:76641000-76648200	Weak transcription	Brain Cingulate Gyrus	brain
21	chr4:76641000-76648200	Weak transcription	Fetal Intestine Small	intestine
22	chr4:76641000-76648200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr4:76641200-76647800	Weak transcription	Brain Angular Gyrus	brain
24	chr4:76641200-76647800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr4:76641200-76648000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr4:76641200-76648200	Weak transcription	NHDF-Ad	bronchial
27	chr4:76641400-76648200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr4:76641400-76648200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr4:76641400-76648400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr4:76641400-76648400	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr4:76641400-76648600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr4:76641400-76648800	Weak transcription	Right Ventricle	heart
33	chr4:76642600-76647800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr4:76642800-76647800	Weak transcription	Esophagus	oesophagus
35	chr4:76642800-76647800	Weak transcription	Fetal Stomach	stomach
36	chr4:76642800-76647800	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr4:76643000-76648400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr4:76643200-76647800	Weak transcription	Psoas Muscle	Psoas
39	chr4:76643200-76648400	Weak transcription	Left Ventricle	heart
40	chr4:76644000-76649200	Weak transcription	Gastric	stomach
41	chr4:76644200-76647800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr4:76644200-76647800	Weak transcription	HMEC	breast
43	chr4:76644200-76647800	Weak transcription	HUVEC	blood vessel
44	chr4:76644200-76648400	Weak transcription	Pancreas	Pancrea
45	chr4:76645400-76648200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr4:76645400-76648200	Weak transcription	Primary B cells from peripheral blood	blood
47	chr4:76645600-76648200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr4:76646800-76647800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr4:76647000-76647800	Enhancers	HepG2	liver
50	chr4:76647000-76648400	Enhancers	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links