Variant report

Variant	rs2659541
Chromosome Location	chr4:102118308-102118309
allele	A/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	POLR2A	chr4:102118223-102118742	MCF-7	breast:	n/a	n/a
2	KAP1	chr4:102117805-102118521	HEK293	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:102112038..102115219-chr4:102118263..102121528,3	MCF-7	breast:

Variant related genes	Relation type
PPP3CA	TF binding region

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1021965	0.85[ASN][1000 genomes]
rs1157038	0.90[CEU][hapmap]
rs1354785	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1395475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1395476	0.90[CEU][hapmap];0.85[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs1506799	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1506800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1506802	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1506803	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1506804	0.89[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs1543856	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17030851	0.81[ASN][1000 genomes]
rs2135609	0.90[CEU][hapmap]
rs2135610	0.90[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs2135612	0.89[CEU][hapmap]
rs2135614	0.80[ASN][1000 genomes]
rs2174683	0.80[ASN][1000 genomes]
rs2659503	0.90[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs2659504	0.89[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs2659505	0.85[CEU][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs2659506	0.93[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2659508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2659509	0.81[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap];0.82[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2659511	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2659512	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2659513	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2659522	0.89[CEU][hapmap]
rs2659525	0.90[CEU][hapmap]
rs2659530	0.90[CEU][hapmap]
rs2659531	0.89[CEU][hapmap]
rs2659532	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2659533	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2659534	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2659537	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2659538	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2659539	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2659540	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2659542	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2850347	0.80[CEU][hapmap]
rs2850365	0.80[CEU][hapmap]
rs2850951	0.80[CEU][hapmap]
rs2850980	0.85[ASN][1000 genomes]
rs2850981	0.90[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs2850982	0.89[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs2850985	0.91[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2850987	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2850989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2850990	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2850991	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2850994	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2850995	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2850998	0.90[CEU][hapmap]
rs2851003	0.90[CEU][hapmap]
rs3804366	1.00[CEU][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4478191	0.90[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs73833252	0.83[ASN][1000 genomes]
rs931871	0.85[CHB][hapmap];0.80[ASN][1000 genomes]
rs970071	0.90[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931418	chr4:101500167-102443207	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv999741	chr4:102009017-102454115	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537199	chr4:102009017-102454115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1004766	chr4:102009017-102713765	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537200	chr4:102009017-102713765	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1011351	chr4:102056024-102450302	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102098600-102118600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr4:102104400-102119400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr4:102104400-102119600	Weak transcription	Primary T cells from cord blood	blood
4	chr4:102104400-102119600	Weak transcription	Ovary	ovary
5	chr4:102105400-102126200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr4:102106200-102121600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr4:102107600-102126600	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr4:102109200-102126200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr4:102109600-102119400	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr4:102109800-102122600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr4:102111200-102122400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr4:102111800-102119600	Weak transcription	Fetal Brain Female	brain
13	chr4:102113200-102118600	Weak transcription	Lung	lung
14	chr4:102113200-102119800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr4:102113200-102119800	Weak transcription	Fetal Brain Male	brain
16	chr4:102113200-102121000	Weak transcription	HSMM	muscle
17	chr4:102113200-102122400	Weak transcription	Aorta	Aorta
18	chr4:102113200-102124400	Weak transcription	Pancreas	Pancrea
19	chr4:102113400-102120400	Weak transcription	Fetal Heart	heart
20	chr4:102113400-102120800	Weak transcription	NH-A	brain
21	chr4:102113600-102119400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr4:102113600-102119600	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr4:102113600-102119600	Weak transcription	Brain Angular Gyrus	brain
24	chr4:102113600-102120600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr4:102113600-102120800	Weak transcription	Right Ventricle	heart
26	chr4:102113600-102121400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr4:102113600-102122800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr4:102113800-102118400	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr4:102113800-102118600	Weak transcription	Fetal Muscle Leg	muscle
30	chr4:102113800-102119600	Weak transcription	Brain Hippocampus Middle	brain
31	chr4:102113800-102119600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr4:102113800-102119600	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr4:102113800-102119600	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr4:102113800-102119800	Weak transcription	Fetal Kidney	kidney
35	chr4:102113800-102120400	Weak transcription	Brain Substantia Nigra	brain
36	chr4:102113800-102120600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr4:102113800-102120800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr4:102113800-102121000	Weak transcription	Stomach Smooth Muscle	stomach
39	chr4:102113800-102121000	Weak transcription	HMEC	breast
40	chr4:102113800-102122800	Weak transcription	Right Atrium	heart
41	chr4:102113800-102126200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr4:102113800-102127200	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr4:102113800-102131800	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr4:102114000-102119800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr4:102114000-102120000	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr4:102114000-102120600	Weak transcription	NHDF-Ad	bronchial
47	chr4:102114000-102121200	Weak transcription	Adipose Nuclei	Adipose
48	chr4:102114200-102118400	Strong transcription	Primary B cells from cord blood	blood
49	chr4:102114200-102119200	Weak transcription	Brain Anterior Caudate	brain
50	chr4:102114200-102119400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links