Variant report

Variant	rs13063594
Chromosome Location	chr3:99603697-99603698
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:99596053..99600789-chr3:99601531..99605674,5	MCF-7	breast:
2	chr3:99603110..99605515-chr3:99787025..99789865,2	MCF-7	breast:
3	chr3:99603421..99605877-chr3:99613161..99615005,2	MCF-7	breast:
4	chr3:99601766..99603960-chr3:99724495..99726434,2	MCF-7	breast:
5	chr3:99602517..99605057-chr7:140621979..140624575,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000157764	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs13060898	1.00[JPT][hapmap]
rs13073356	1.00[JPT][hapmap]
rs13074107	1.00[JPT][hapmap]
rs13076199	0.87[EUR][1000 genomes]
rs13081855	1.00[JPT][hapmap]
rs13082013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13084413	1.00[CEU][hapmap]
rs13089461	0.87[EUR][1000 genomes]
rs13095282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13096116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13097830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13100490	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17778253	1.00[JPT][hapmap]
rs34174004	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34571898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34971126	0.82[AMR][1000 genomes]
rs35074168	1.00[AFR][1000 genomes]
rs35098023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35669249	1.00[AFR][1000 genomes]
rs36077012	0.87[EUR][1000 genomes]
rs62283494	1.00[AFR][1000 genomes]
rs62283538	0.82[EUR][1000 genomes]
rs6788894	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6791889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7626245	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7636514	1.00[JPT][hapmap]
rs7647466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7649862	1.00[CEU][hapmap];1.00[JPT][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	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv822194	chr3:99600260-99604375	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99595400-99608400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr3:99595600-99607400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr3:99595600-99612800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr3:99596600-99614200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:99597200-99614200	Weak transcription	HMEC	breast
6	chr3:99600800-99638600	Weak transcription	Left Ventricle	heart
7	chr3:99601800-99604800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr3:99602000-99604600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr3:99602000-99605400	Enhancers	HepG2	liver
10	chr3:99602400-99604200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr3:99602600-99604200	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr3:99602600-99604600	Enhancers	Primary T cells from cord blood	blood
13	chr3:99602600-99604800	Enhancers	Fetal Intestine Large	intestine
14	chr3:99602600-99605000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:99602800-99604000	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr3:99602800-99604000	Enhancers	K562	blood
17	chr3:99602800-99604200	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr3:99602800-99604200	Enhancers	NHEK	skin
19	chr3:99602800-99604600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr3:99603000-99603800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr3:99603000-99604000	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr3:99603000-99604200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr3:99603000-99604200	Enhancers	Duodenum Mucosa	Duodenum
24	chr3:99603000-99604400	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr3:99603000-99605400	Enhancers	Stomach Mucosa	stomach
26	chr3:99603200-99603800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr3:99603200-99603800	Flanking Active TSS	HUVEC	blood vessel
28	chr3:99603200-99604000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr3:99603200-99604000	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr3:99603200-99604000	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr3:99603200-99604200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:99603200-99604200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr3:99603400-99603800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:99603400-99603800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr3:99603400-99603800	Enhancers	Brain Anterior Caudate	brain
36	chr3:99603400-99604000	Enhancers	Primary hematopoietic stem cells	blood
37	chr3:99603400-99604000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr3:99603400-99604000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr3:99603400-99604200	Enhancers	Small Intestine	intestine
40	chr3:99603400-99604400	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr3:99603400-99604800	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr3:99603400-99605000	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr3:99603400-99605400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr3:99603400-99609400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr3:99603600-99603800	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr3:99603600-99603800	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr3:99603600-99604200	Enhancers	Rectal Mucosa Donor 29	rectum
48	chr3:99603600-99611200	Weak transcription	Psoas Muscle	Psoas

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