Variant report

Variant	rs4690072
Chromosome Location	chr4:3122507-3122508
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:3112475..3121644-chr4:3122211..3126506,10	MCF-7	breast:
2	chr4:3119274..3122610-chr4:3124266..3127646,4	K562	blood:

Variant related genes	Relation type
ENSG00000197386	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10012793	0.86[AFR][1000 genomes]
rs110501	0.96[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs16843804	1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs16843836	0.96[ASN][1000 genomes]
rs17780797	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1891701	0.83[ASN][1000 genomes]
rs2024115	0.84[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2071655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2071662	0.84[EUR][1000 genomes]
rs2071704	0.88[CEU][hapmap]
rs2237006	0.82[EUR][1000 genomes]
rs2285086	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2285087	0.85[ASN][1000 genomes]
rs2298971	0.88[EUR][1000 genomes]
rs28403215	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28867436	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs362273	0.81[JPT][hapmap]
rs362306	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs362319	0.84[EUR][1000 genomes]
rs362331	0.96[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.87[EUR][1000 genomes]
rs363063	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs363064	1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs363066	1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs363091	0.93[YRI][hapmap]
rs363092	0.89[EUR][1000 genomes]
rs363096	1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs363106	0.90[YRI][hapmap];0.83[AFR][1000 genomes]
rs3856973	1.00[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3905238	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4690011	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4690071	0.85[ASN][1000 genomes]
rs4690073	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55962025	0.96[ASN][1000 genomes]
rs59147561	0.84[AFR][1000 genomes]
rs59613878	0.82[ASN][1000 genomes]
rs60197694	0.83[ASN][1000 genomes]
rs61348208	0.85[ASN][1000 genomes]
rs61792530	0.85[ASN][1000 genomes]
rs6446722	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6446723	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6828615	0.86[AFR][1000 genomes]
rs6834455	0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs6843895	0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs6844859	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap];0.88[EUR][1000 genomes]
rs6855981	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73191188	0.86[ASN][1000 genomes]
rs7659144	1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs7665816	0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs7685686	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes]
rs7688390	0.87[AFR][1000 genomes]
rs7691627	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs82333	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs916171	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.88[EUR][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	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv461163	chr4:2906285-3234980	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv593437	chr4:2906285-3234980	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3088200-3164200	Strong transcription	Primary monocytes fromperipheralblood	blood
2	chr4:3094400-3123400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr4:3097200-3143400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr4:3097200-3162200	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr4:3097400-3163800	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr4:3098000-3162600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:3100000-3159400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr4:3101000-3122600	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr4:3101000-3124200	Strong transcription	Fetal Intestine Large	intestine
10	chr4:3101000-3124400	Strong transcription	Thymus	Thymus
11	chr4:3101600-3124200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr4:3105400-3123800	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr4:3105400-3124800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr4:3106400-3123400	Strong transcription	Primary T cells from cord blood	blood
15	chr4:3106400-3123800	Strong transcription	Fetal Thymus	thymus
16	chr4:3106400-3145000	Strong transcription	Dnd41	blood
17	chr4:3106800-3125200	Strong transcription	Primary B cells from cord blood	blood
18	chr4:3108400-3123000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr4:3108600-3125800	Strong transcription	Primary B cells from peripheral blood	blood
20	chr4:3108600-3136600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr4:3108600-3163000	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr4:3108800-3123600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr4:3108800-3164600	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr4:3109000-3123200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr4:3109000-3123600	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr4:3109000-3124200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr4:3109200-3123200	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr4:3109200-3142600	Strong transcription	GM12878-XiMat	blood
29	chr4:3109400-3124600	Strong transcription	Duodenum Mucosa	Duodenum
30	chr4:3109400-3130400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr4:3110400-3123400	Weak transcription	Stomach Mucosa	stomach
32	chr4:3110600-3123400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr4:3111600-3125400	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr4:3112600-3124200	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr4:3112800-3124200	Strong transcription	H9 Cell Line	embryonic stem cell
36	chr4:3113800-3124200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr4:3114600-3292400	Weak transcription	Right Atrium	heart
38	chr4:3114800-3162800	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr4:3115000-3123000	Strong transcription	Fetal Muscle Leg	muscle
40	chr4:3115800-3143400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr4:3115800-3161600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr4:3115800-3162800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr4:3116000-3136200	Strong transcription	Liver	Liver
44	chr4:3116200-3123000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr4:3116600-3123000	Strong transcription	Primary hematopoietic stem cells	blood
46	chr4:3116600-3124200	Strong transcription	Brain Angular Gyrus	brain
47	chr4:3116600-3124400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr4:3116600-3124800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr4:3116800-3124200	Strong transcription	Brain Germinal Matrix	brain
50	chr4:3116800-3126000	Strong transcription	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links