Variant report

Variant	rs6438147
Chromosome Location	chr3:113128342-113128343
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	chr3:113121878..113125300-chr3:113126729..113129610,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000206530	Chromatin interaction
ENSG00000243849	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10934228	0.81[JPT][hapmap];0.90[AMR][1000 genomes]
rs11715198	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12488964	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12635786	0.87[CHB][hapmap]
rs12636607	0.83[CHB][hapmap]
rs13091945	0.83[AMR][1000 genomes]
rs17321330	0.92[CEU][hapmap];0.86[CHB][hapmap]
rs1906142	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1979554	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2054823	0.95[CEU][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2129430	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2171293	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2895413	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35581027	0.87[EUR][1000 genomes]
rs35935366	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3732806	0.83[CHB][hapmap]
rs4682138	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4682486	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6438140	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6438143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6438144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6438145	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6438146	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6438148	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66524865	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6768117	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6769970	0.83[CHB][hapmap];0.87[YRI][hapmap]
rs6775574	0.96[CEU][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6777880	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6805691	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7617772	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7618884	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7621210	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7623122	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7623389	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7625841	0.96[CEU][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7631730	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7633428	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7642163	0.85[EUR][1000 genomes]
rs7646985	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7650538	0.96[CEU][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs775232	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs775233	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9682734	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9815835	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9840124	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9848087	0.96[CEU][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9866748	0.96[CEU][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9869141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9870996	0.83[YRI][hapmap]
rs9990291	0.84[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	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1004000	chr3:113116778-113513899	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6438147	SIDT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113074400-113184400	Weak transcription	Hela-S3	cervix
2	chr3:113080800-113143800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr3:113092400-113134200	Weak transcription	Fetal Kidney	kidney
4	chr3:113093600-113134800	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr3:113098800-113134800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr3:113099000-113134800	Weak transcription	A549	lung
7	chr3:113099600-113144800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:113102200-113148800	Weak transcription	Brain Angular Gyrus	brain
9	chr3:113102400-113144400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:113106800-113143600	Weak transcription	Dnd41	blood
11	chr3:113107000-113137000	Weak transcription	Esophagus	oesophagus
12	chr3:113107200-113145200	Weak transcription	Aorta	Aorta
13	chr3:113107600-113138200	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr3:113109200-113159800	Weak transcription	Brain Hippocampus Middle	brain
15	chr3:113111600-113146400	Weak transcription	Brain Substantia Nigra	brain
16	chr3:113112200-113148400	Weak transcription	Brain Anterior Caudate	brain
17	chr3:113113000-113145600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr3:113114000-113143800	Weak transcription	Fetal Thymus	thymus
19	chr3:113117600-113148400	Weak transcription	Placenta	Placenta
20	chr3:113118000-113134800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr3:113119400-113129600	Weak transcription	Psoas Muscle	Psoas
22	chr3:113119600-113145200	Weak transcription	Lung	lung
23	chr3:113121400-113128600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr3:113121600-113134600	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr3:113122200-113128400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr3:113122400-113138400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr3:113122400-113144800	Weak transcription	Pancreas	Pancrea
28	chr3:113122800-113130800	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr3:113122800-113134200	Weak transcription	Primary hematopoietic stem cells	blood
30	chr3:113122800-113138000	Weak transcription	Stomach Smooth Muscle	stomach
31	chr3:113122800-113138600	Weak transcription	Primary B cells from cord blood	blood
32	chr3:113122800-113144000	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr3:113122800-113144000	Weak transcription	Thymus	Thymus
34	chr3:113122800-113144800	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr3:113123000-113133600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:113123000-113133600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:113123000-113134000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr3:113123000-113134800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr3:113123000-113143600	Weak transcription	Left Ventricle	heart
40	chr3:113123000-113144400	Weak transcription	HSMM	muscle
41	chr3:113123200-113143800	Weak transcription	Ovary	ovary
42	chr3:113123600-113143200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr3:113123800-113134800	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr3:113124400-113129800	Weak transcription	Liver	Liver
45	chr3:113124600-113143600	Weak transcription	Colon Smooth Muscle	Colon
46	chr3:113124800-113133600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:113125000-113138000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links