Variant report

Variant	rs3735440
Chromosome Location	chr7:21551070-21551071
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:21550742..21552749-chr7:21554264..21556161,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1013716	0.82[CHD][hapmap]
rs10269168	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10272006	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11971316	1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs11983472	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12668354	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12672629	0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12673091	0.86[CHD][hapmap]
rs12673975	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2158414	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2282888	0.83[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2390539	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28541530	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs40245	0.83[CEU][hapmap];0.82[JPT][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes]
rs41495348	0.90[MEX][hapmap];0.85[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4397283	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4722031	0.92[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6461561	0.86[ASW][hapmap];0.83[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6461562	0.83[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs6461565	0.83[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap]
rs6461567	0.91[CEU][hapmap];0.81[ASN][1000 genomes]
rs6461568	0.84[CEU][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6948810	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6974974	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6978922	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7780553	0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7781732	0.86[CEU][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7792280	0.81[CEU][hapmap]
rs7796796	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7798894	0.87[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7810841	1.00[CEU][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7811417	0.92[CEU][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs7811539	0.93[CHD][hapmap]
rs9639377	1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs9639378	0.83[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027302	chr7:21391598-21727016	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv538800	chr7:21391598-21727016	Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1028434	chr7:21468437-21636671	ZNF genes & repeats Strong transcription Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv1023655	chr7:21486485-21727016	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv538801	chr7:21486485-21727016	ZNF genes & repeats Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv830921	chr7:21489100-21688016	Strong transcription ZNF genes & repeats Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
7	nsv1030577	chr7:21548909-21681379	Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3735440	MACC1	cis	cerebellum	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:21487400-21557000	Weak transcription	Aorta	Aorta
2	chr7:21500000-21552800	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr7:21516200-21556400	Weak transcription	Brain Substantia Nigra	brain
4	chr7:21517000-21556000	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr7:21520800-21552800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr7:21521200-21552600	Weak transcription	Brain Angular Gyrus	brain
7	chr7:21536600-21557000	Weak transcription	Psoas Muscle	Psoas
8	chr7:21536800-21552800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr7:21538800-21555000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr7:21539200-21552600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr7:21539600-21554800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr7:21539600-21555800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr7:21539800-21551600	Strong transcription	Primary B cells from cord blood	blood
14	chr7:21540600-21551600	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr7:21540600-21554400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr7:21540800-21551400	Weak transcription	Brain Anterior Caudate	brain
17	chr7:21541000-21554800	Weak transcription	Lung	lung
18	chr7:21542000-21551200	Weak transcription	Fetal Kidney	kidney
19	chr7:21542200-21552200	Weak transcription	Adipose Nuclei	Adipose
20	chr7:21545400-21552600	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr7:21546000-21552200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr7:21546200-21552000	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr7:21546800-21553800	Strong transcription	Primary B cells from peripheral blood	blood
24	chr7:21547000-21551600	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr7:21547800-21552000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr7:21547800-21554000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr7:21548000-21552600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr7:21548400-21552200	Weak transcription	Brain Hippocampus Middle	brain
29	chr7:21548400-21552400	Weak transcription	Fetal Stomach	stomach
30	chr7:21548400-21552600	Weak transcription	Fetal Muscle Leg	muscle
31	chr7:21548400-21553200	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr7:21548400-21556600	Weak transcription	Thymus	Thymus
33	chr7:21548600-21552600	Weak transcription	Ovary	ovary
34	chr7:21548800-21551400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr7:21548800-21551800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr7:21549000-21551600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr7:21549000-21556400	Weak transcription	Primary T cells from cord blood	blood
38	chr7:21549200-21551200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr7:21549200-21551600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr7:21549200-21552400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr7:21549400-21551200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr7:21549400-21551800	Weak transcription	Duodenum Mucosa	Duodenum
43	chr7:21549400-21552000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr7:21549400-21552000	Strong transcription	Primary hematopoietic stem cells	blood
45	chr7:21549400-21554800	Weak transcription	Fetal Brain Female	brain
46	chr7:21549600-21551600	Strong transcription	Dnd41	blood
47	chr7:21549800-21553000	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr7:21550000-21551200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr7:21550200-21552000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr7:21550400-21551400	Strong transcription	GM12878-XiMat	blood

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