Variant report

Variant	rs1888959
Chromosome Location	chr6:131335324-131335325
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	ZNF384	chr6:131335184-131335374	K562	blood:	n/a	n/a
2	CEBPB	chr6:131335281-131336411	Hela-S3	cervix:	n/a	chr6:131335692-131335703 chr6:131335418-131335429

Variant related genes	Relation type
EPB41L2	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1332490	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1332491	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1338905	0.89[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1855077	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1976982	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2007339	0.89[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2151069	0.84[CEU][hapmap]
rs2225557	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4895902	1.00[CEU][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4897480	0.92[EUR][1000 genomes]
rs4897481	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4897482	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4897488	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4897490	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6569716	0.84[CEU][hapmap];0.81[GIH][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs6569718	0.89[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6569720	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs6569722	0.86[EUR][1000 genomes]
rs6569725	0.84[EUR][1000 genomes]
rs6900810	0.89[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6908917	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6909134	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6928986	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6942081	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7742376	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7765007	0.89[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7765757	0.89[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs9321268	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9372988	0.89[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9689026	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032955	chr6:131298803-131818502	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv538443	chr6:131298803-131818502	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131329800-131336400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:131329800-131347400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:131330200-131335400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:131330400-131336400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr6:131332200-131345400	Weak transcription	Left Ventricle	heart
6	chr6:131332800-131339600	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr6:131333400-131335400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr6:131333600-131339200	Weak transcription	Pancreas	Pancrea
9	chr6:131333800-131337400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr6:131334000-131337000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr6:131334000-131337400	Enhancers	Fetal Kidney	kidney
12	chr6:131334400-131335400	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr6:131334400-131335400	Enhancers	NH-A	brain
14	chr6:131334400-131335800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr6:131334400-131337200	Weak transcription	Small Intestine	intestine
16	chr6:131334400-131337400	Enhancers	HMEC	breast
17	chr6:131334600-131335400	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr6:131334600-131335400	Flanking Active TSS	HUVEC	blood vessel
19	chr6:131334600-131335600	Enhancers	Primary hematopoietic stem cells	blood
20	chr6:131334600-131335600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr6:131334600-131335800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:131334600-131336600	Enhancers	Dnd41	blood
23	chr6:131334600-131338000	Enhancers	Fetal Stomach	stomach
24	chr6:131334600-131338200	Enhancers	HepG2	liver
25	chr6:131334600-131338200	Enhancers	Osteobl	bone
26	chr6:131334600-131339000	Enhancers	Rectal Smooth Muscle	rectum
27	chr6:131334800-131335400	Flanking Active TSS	Colon Smooth Muscle	Colon
28	chr6:131334800-131335800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr6:131334800-131335800	Flanking Active TSS	Brain Anterior Caudate	brain
30	chr6:131334800-131336600	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr6:131334800-131336600	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr6:131334800-131336800	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr6:131334800-131336800	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr6:131334800-131337400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr6:131334800-131337600	Enhancers	A549	lung
36	chr6:131334800-131342800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr6:131335000-131335600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr6:131335000-131336000	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr6:131335000-131336000	Weak transcription	Liver	Liver
40	chr6:131335000-131336800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr6:131335000-131337000	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr6:131335000-131337200	Weak transcription	HSMMtube	muscle
43	chr6:131335000-131337800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr6:131335000-131338000	Enhancers	HSMM	muscle
45	chr6:131335200-131335400	Flanking Active TSS	Brain Angular Gyrus	brain
46	chr6:131335200-131335400	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr6:131335200-131335400	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr6:131335200-131335800	Enhancers	Fetal Muscle Leg	muscle
49	chr6:131335200-131336000	Enhancers	Ovary	ovary
50	chr6:131335200-131336200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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