Variant report

Variant	rs6825104
Chromosome Location	chr4:48629767-48629768
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	chr4:48628287..48631259-chr4:48635735..48637672,2	MCF-7	breast:
2	chr4:48622239..48624002-chr4:48627725..48630280,2	K562	blood:

Variant related genes	Relation type
ENSG00000075539	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10517225	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11727472	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12498166	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12505376	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12506770	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12508327	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12509766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13110719	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13134960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1517675	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs1565218	0.91[ASN][1000 genomes]
rs16861344	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16861347	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1702795	0.86[AMR][1000 genomes]
rs1702800	1.00[ASN][1000 genomes]
rs1712762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17609740	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17609761	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17656189	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17656212	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17656255	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1814784	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1850520	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28581223	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2945331	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3107023	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4235156	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4610307	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695388	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695389	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55730515	0.91[ASN][1000 genomes]
rs55884608	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55986500	0.91[ASN][1000 genomes]
rs57893769	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447646	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447648	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6829709	1.00[YRI][hapmap]
rs6852840	0.91[ASN][1000 genomes]
rs707719	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73814762	0.91[ASN][1000 genomes]
rs73814763	0.91[ASN][1000 genomes]
rs73814782	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73814798	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73817807	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73817808	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73817809	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73817826	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73817827	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7690681	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7693468	0.91[ASN][1000 genomes]
rs7695730	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7695813	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs776582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs776586	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs776593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs776594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs776596	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs776597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs776598	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs776599	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs938790	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[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	nsv829925	chr4:48467693-48639342	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48563000-48637400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:48575200-48643000	Weak transcription	HSMMtube	muscle
3	chr4:48578600-48637000	Weak transcription	Esophagus	oesophagus
4	chr4:48588400-48644600	Weak transcription	Colon Smooth Muscle	Colon
5	chr4:48594000-48637400	Weak transcription	Spleen	Spleen
6	chr4:48597800-48644600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr4:48598200-48634800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr4:48606800-48637800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:48606800-48645000	Weak transcription	Gastric	stomach
10	chr4:48609800-48637000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr4:48614600-48637000	Weak transcription	Small Intestine	intestine
12	chr4:48620200-48634800	Weak transcription	Aorta	Aorta
13	chr4:48620200-48634800	Weak transcription	Left Ventricle	heart
14	chr4:48620200-48637000	Weak transcription	Fetal Lung	lung
15	chr4:48620200-48637400	Weak transcription	Pancreas	Pancrea
16	chr4:48620200-48644800	Weak transcription	Fetal Stomach	stomach
17	chr4:48620400-48634800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr4:48620600-48635800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr4:48621200-48637200	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr4:48621200-48642400	Weak transcription	Fetal Heart	heart
21	chr4:48621200-48729400	Weak transcription	Thymus	Thymus
22	chr4:48621600-48634800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr4:48621800-48635000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr4:48621800-48637400	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr4:48621800-48642200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr4:48621800-48645000	Weak transcription	Lung	lung
27	chr4:48621800-48655800	Weak transcription	Colonic Mucosa	Colon
28	chr4:48622800-48631800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr4:48622800-48637000	Weak transcription	Adipose Nuclei	Adipose
30	chr4:48622800-48637600	Weak transcription	Liver	Liver
31	chr4:48622800-48644800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr4:48622800-48648400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr4:48623000-48631400	Weak transcription	HUVEC	blood vessel
34	chr4:48623000-48634800	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr4:48623000-48635600	Weak transcription	NHDF-Ad	bronchial
36	chr4:48623200-48634800	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr4:48623200-48637000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr4:48623200-48637000	Weak transcription	Psoas Muscle	Psoas
39	chr4:48623200-48637000	Weak transcription	GM12878-XiMat	blood
40	chr4:48623200-48637400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr4:48623200-48637600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr4:48623200-48638200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr4:48623400-48631400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr4:48623400-48634800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr4:48623400-48635000	Weak transcription	Brain Anterior Caudate	brain
46	chr4:48623400-48635800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr4:48623400-48637400	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr4:48623400-48644400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr4:48623600-48631200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr4:48623600-48635000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links