Variant report

Variant	rs6447657
Chromosome Location	chr4:48752551-48752552
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48751207..48753110-chr4:48754694..48756381,2	MCF-7	breast:

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10029425	1.00[AMR][1000 genomes]
rs10034207	1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10049760	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs10755182	1.00[AMR][1000 genomes]
rs10805171	1.00[AMR][1000 genomes]
rs10805172	0.87[YRI][hapmap];1.00[AMR][1000 genomes]
rs10938535	1.00[AMR][1000 genomes]
rs10938538	1.00[AMR][1000 genomes]
rs10938539	1.00[AMR][1000 genomes]
rs10938541	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12500224	1.00[AMR][1000 genomes]
rs12500244	1.00[AMR][1000 genomes]
rs12507475	1.00[AMR][1000 genomes]
rs12507546	1.00[AMR][1000 genomes]
rs1474072	1.00[AMR][1000 genomes]
rs1517673	1.00[AMR][1000 genomes]
rs1517676	1.00[AMR][1000 genomes]
rs1517677	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1533511	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1554257	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1616561	1.00[AMR][1000 genomes]
rs1702796	1.00[AMR][1000 genomes]
rs1702799	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs1712762	1.00[YRI][hapmap]
rs1712771	1.00[AMR][1000 genomes]
rs1949422	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2138866	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2138867	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2572342	0.82[YRI][hapmap]
rs28371079	1.00[AMR][1000 genomes]
rs2883410	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2940319	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs4235155	0.87[YRI][hapmap];1.00[AMR][1000 genomes]
rs4235157	1.00[AMR][1000 genomes]
rs4330326	1.00[AMR][1000 genomes]
rs4558842	1.00[AMR][1000 genomes]
rs4694896	1.00[AMR][1000 genomes]
rs4694898	1.00[AMR][1000 genomes]
rs4694903	1.00[AMR][1000 genomes]
rs4695385	1.00[AMR][1000 genomes]
rs4695386	1.00[AMR][1000 genomes]
rs4695390	1.00[AMR][1000 genomes]
rs4695402	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4695403	1.00[AMR][1000 genomes]
rs4695405	1.00[AMR][1000 genomes]
rs4695406	0.82[YRI][hapmap]
rs6447642	1.00[AMR][1000 genomes]
rs6447654	1.00[AMR][1000 genomes]
rs6447656	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6821456	1.00[AMR][1000 genomes]
rs6823351	1.00[AMR][1000 genomes]
rs6827481	1.00[AMR][1000 genomes]
rs6828500	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6835757	1.00[AMR][1000 genomes]
rs6844088	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6846797	1.00[AMR][1000 genomes]
rs6848222	1.00[AMR][1000 genomes]
rs6848417	1.00[AMR][1000 genomes]
rs6853876	1.00[AMR][1000 genomes]
rs707720	1.00[AMR][1000 genomes]
rs7434721	1.00[AMR][1000 genomes]
rs7664507	1.00[AMR][1000 genomes]
rs7689293	0.87[YRI][hapmap];1.00[AMR][1000 genomes]
rs7689662	1.00[AMR][1000 genomes]
rs7692480	1.00[AMR][1000 genomes]
rs7698064	1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs776581	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs776583	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs776587	1.00[AMR][1000 genomes]
rs776589	1.00[AMR][1000 genomes]
rs776595	0.82[YRI][hapmap];1.00[AMR][1000 genomes]
rs776603	1.00[AMR][1000 genomes]
rs938789	0.83[AFR][1000 genomes]
rs938791	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs9994214	1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9997932	1.00[AMR][1000 genomes]
rs9998178	1.00[YRI][hapmap];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002674	chr4:48507608-49032909	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv537087	chr4:48507608-49032909	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1010923	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv537088	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1013762	chr4:48580484-49032909	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv537089	chr4:48580484-49032909	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	esv1792683	chr4:48686817-48764009	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv1795181	chr4:48686817-48764009	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv1793455	chr4:48686817-48859142	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv1010381	chr4:48701525-49309842	Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
11	esv1792281	chr4:48719424-48764009	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	esv1794245	chr4:48719424-48764009	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	esv1794757	chr4:48719424-48764009	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv594137	chr4:48748305-48763163	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48731600-48779800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:48742000-48758800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr4:48742000-48768400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr4:48742600-48768200	Weak transcription	Pancreas	Pancrea
5	chr4:48742800-48753800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr4:48744600-48752800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr4:48744600-48753000	Weak transcription	Osteobl	bone
8	chr4:48744800-48753600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr4:48745000-48765200	Weak transcription	Primary B cells from cord blood	blood
10	chr4:48747200-48754800	Weak transcription	Fetal Stomach	stomach
11	chr4:48747200-48777200	Weak transcription	Fetal Intestine Small	intestine
12	chr4:48747400-48767800	Weak transcription	Fetal Intestine Large	intestine
13	chr4:48748600-48756400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr4:48749000-48757200	Weak transcription	Gastric	stomach
15	chr4:48749200-48761400	Weak transcription	Thymus	Thymus
16	chr4:48749200-48768200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr4:48750000-48754200	Weak transcription	HMEC	breast
18	chr4:48750000-48754200	Weak transcription	NHEK	skin
19	chr4:48750200-48754200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr4:48750400-48753400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr4:48751000-48753600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr4:48751000-48754000	Enhancers	Brain Hippocampus Middle	brain
23	chr4:48751000-48768400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr4:48751200-48752800	Weak transcription	Primary hematopoietic stem cells	blood
25	chr4:48751200-48754200	Weak transcription	Duodenum Mucosa	Duodenum
26	chr4:48751400-48752800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr4:48751400-48753000	Weak transcription	Primary T cells from cord blood	blood
28	chr4:48751400-48753200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr4:48751400-48758800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr4:48751600-48752800	Weak transcription	Adipose Nuclei	Adipose
31	chr4:48751600-48752800	Weak transcription	Brain Substantia Nigra	brain
32	chr4:48751600-48753400	Weak transcription	Brain Anterior Caudate	brain
33	chr4:48751600-48753600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr4:48751600-48753800	Weak transcription	GM12878-XiMat	blood
35	chr4:48751600-48754000	Weak transcription	K562	blood
36	chr4:48751600-48754600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr4:48751600-48754800	Weak transcription	Stomach Smooth Muscle	stomach
38	chr4:48751600-48761400	Weak transcription	Dnd41	blood
39	chr4:48751600-48777200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr4:48751800-48752800	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr4:48751800-48752800	Weak transcription	Brain Angular Gyrus	brain
42	chr4:48751800-48752800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr4:48751800-48752800	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr4:48751800-48753800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr4:48751800-48753800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr4:48751800-48754800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr4:48751800-48754800	Weak transcription	Aorta	Aorta
48	chr4:48751800-48763800	Weak transcription	Spleen	Spleen
49	chr4:48751800-48763800	Weak transcription	HSMM	muscle
50	chr4:48752000-48752800	Weak transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links