Variant report

Variant	rs3801135
Chromosome Location	chr7:38858256-38858257
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:38857572..38859924-chr7:38860336..38863164,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10242978	0.82[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs10247503	0.81[JPT][hapmap]
rs10259755	0.85[AFR][1000 genomes]
rs10272767	0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs12532461	0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs1473137	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs1859937	0.82[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2074656	0.85[CEU][hapmap];0.86[CHB][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2190666	0.81[CHB][hapmap]
rs2240350	0.85[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.81[TSI][hapmap]
rs2240351	0.82[JPT][hapmap]
rs2240355	0.85[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs2240555	0.85[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap]
rs2286081	0.85[CEU][hapmap];0.95[CHB][hapmap];0.92[EUR][1000 genomes]
rs2286086	0.82[CHB][hapmap]
rs2286090	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2286092	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2286095	0.85[CEU][hapmap];0.94[CHB][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2286097	0.85[CEU][hapmap];0.95[CHB][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2286099	0.88[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2286100	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2286106	0.81[JPT][hapmap]
rs2392609	0.81[CHB][hapmap];0.91[JPT][hapmap];0.87[YRI][hapmap]
rs2893567	1.00[ASW][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.94[LWK][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes]
rs3779126	0.85[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.85[LWK][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3801142	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3801143	0.82[JPT][hapmap]
rs3801144	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3801145	0.82[JPT][hapmap]
rs4430003	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4720299	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4723793	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6462862	0.85[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.85[LWK][hapmap];0.84[MEX][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6961672	0.89[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];0.85[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs733150	0.82[JPT][hapmap]
rs7785161	0.91[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs7785911	0.82[JPT][hapmap]
rs7788664	0.89[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7795874	0.82[JPT][hapmap]
rs7803397	1.00[ASW][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.83[MEX][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes]
rs886646	0.89[CHB][hapmap]
rs9638944	0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap]

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	nsv1032637	chr7:38832627-38902723	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv887966	chr7:38835035-38933942	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3801135	TBX20	cis	parietal	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38793400-38861200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr7:38829400-38864400	Weak transcription	Thymus	Thymus
3	chr7:38829400-38864600	Weak transcription	NHLF	lung
4	chr7:38831000-38871200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr7:38831800-38867800	Weak transcription	Fetal Thymus	thymus
6	chr7:38833400-38859400	Weak transcription	Spleen	Spleen
7	chr7:38834400-38863400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:38835200-38865200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr7:38835600-38862200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr7:38835600-38900800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr7:38835800-38858600	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr7:38839800-38871000	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr7:38842000-38865400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr7:38847400-38869800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr7:38847800-38862400	Weak transcription	Brain Angular Gyrus	brain
16	chr7:38847800-38866800	Weak transcription	Brain Substantia Nigra	brain
17	chr7:38848000-38861200	Weak transcription	Brain Hippocampus Middle	brain
18	chr7:38848200-38861800	Weak transcription	Brain Anterior Caudate	brain
19	chr7:38850200-38865400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr7:38850600-38869600	Weak transcription	Stomach Mucosa	stomach
21	chr7:38851600-38867000	Weak transcription	Gastric	stomach
22	chr7:38851800-38862200	Weak transcription	K562	blood
23	chr7:38852600-38860800	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr7:38852800-38858600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr7:38852800-38858800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr7:38853000-38861000	Strong transcription	Primary B cells from peripheral blood	blood
27	chr7:38853000-38863600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr7:38853200-38859400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr7:38853400-38860800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr7:38853600-38859600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr7:38854000-38870400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr7:38854400-38860600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr7:38854400-38861400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr7:38854600-38858400	Strong transcription	Left Ventricle	heart
35	chr7:38854800-38859000	Strong transcription	Fetal Stomach	stomach
36	chr7:38855200-38858800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr7:38855400-38865400	Weak transcription	Osteobl	bone
38	chr7:38855600-38859000	Strong transcription	Dnd41	blood
39	chr7:38855600-38859400	Strong transcription	Primary T cells from cord blood	blood
40	chr7:38855600-38860600	Strong transcription	Fetal Intestine Large	intestine
41	chr7:38855600-38863200	Strong transcription	Primary B cells from cord blood	blood
42	chr7:38855600-38871000	Weak transcription	HepG2	liver
43	chr7:38855800-38859400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr7:38856000-38859000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr7:38856000-38865200	Weak transcription	NHDF-Ad	bronchial
46	chr7:38856000-38871000	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr7:38856200-38859800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr7:38856200-38865400	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr7:38856200-38871200	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr7:38856400-38859000	Strong transcription	Stomach Smooth Muscle	stomach

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