Variant report

Variant	rs6848417
Chromosome Location	chr4:48592454-48592455
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:48581199..48583322-chr4:48590838..48593348,2	MCF-7	breast:
2	chr4:48590381..48593242-chr4:48779651..48782070,2	K562	blood:
3	chr4:48590381..48593753-chr4:48779651..48782070,3	K562	blood:

Extended variants
information (count: 87 )
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[AMR][1000 genomes]
rs10049760	1.00[AMR][1000 genomes]
rs10755182	1.00[AMR][1000 genomes]
rs10805171	1.00[AMR][1000 genomes]
rs10805172	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10938535	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10938538	1.00[AMR][1000 genomes]
rs10938539	1.00[AMR][1000 genomes]
rs10938541	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]
rs13125379	1.00[AMR][1000 genomes]
rs1474072	1.00[AMR][1000 genomes]
rs1517673	1.00[AMR][1000 genomes]
rs1517676	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1517677	1.00[AMR][1000 genomes]
rs1533511	1.00[AMR][1000 genomes]
rs1554257	1.00[AMR][1000 genomes]
rs1616561	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1702796	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1702799	1.00[AMR][1000 genomes]
rs1712771	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1949422	1.00[AMR][1000 genomes]
rs2138866	1.00[AMR][1000 genomes]
rs2138867	1.00[AMR][1000 genomes]
rs28371079	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28558226	0.90[AFR][1000 genomes]
rs2883410	1.00[AMR][1000 genomes]
rs2940319	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4235155	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4235157	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4330326	1.00[AMR][1000 genomes]
rs4558842	1.00[AMR][1000 genomes]
rs4694896	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4694898	1.00[AMR][1000 genomes]
rs4694903	1.00[AMR][1000 genomes]
rs4695385	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4695386	1.00[AMR][1000 genomes]
rs4695390	1.00[AMR][1000 genomes]
rs4695402	1.00[AMR][1000 genomes]
rs4695403	1.00[AMR][1000 genomes]
rs4695405	1.00[AMR][1000 genomes]
rs4998005	1.00[AMR][1000 genomes]
rs6447642	1.00[AMR][1000 genomes]
rs6447654	1.00[AMR][1000 genomes]
rs6447656	1.00[AMR][1000 genomes]
rs6447657	1.00[AMR][1000 genomes]
rs6821456	1.00[AMR][1000 genomes]
rs6823351	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6827481	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6828500	1.00[AMR][1000 genomes]
rs6835757	1.00[AMR][1000 genomes]
rs6844088	1.00[AMR][1000 genomes]
rs6846797	1.00[AMR][1000 genomes]
rs6848222	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6849798	1.00[AMR][1000 genomes]
rs6853876	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs707720	1.00[AMR][1000 genomes]
rs7434721	1.00[AMR][1000 genomes]
rs7664507	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7689293	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7689662	1.00[AMR][1000 genomes]
rs7692480	1.00[AMR][1000 genomes]
rs7698064	1.00[AMR][1000 genomes]
rs776581	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs776583	1.00[AMR][1000 genomes]
rs776587	1.00[AMR][1000 genomes]
rs776589	1.00[AMR][1000 genomes]
rs776595	1.00[AMR][1000 genomes]
rs776603	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs938791	1.00[AMR][1000 genomes]
rs9994214	1.00[AMR][1000 genomes]
rs9997932	1.00[AMR][1000 genomes]
rs9998178	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470034	chr4:48427773-48605628	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
2	nsv594121	chr4:48427773-48605628	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	nsv966557	chr4:48577320-48618907	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	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
10	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:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48498600-48593000	Strong transcription	Rectal Mucosa Donor 31	rectum
2	chr4:48515800-48625000	Weak transcription	Hela-S3	cervix
3	chr4:48525000-48595600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr4:48528200-48596000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr4:48541200-48594000	Strong transcription	Rectal Mucosa Donor 29	rectum
6	chr4:48542800-48604400	Weak transcription	A549	lung
7	chr4:48545200-48618200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr4:48546400-48596400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr4:48547400-48593600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr4:48557800-48622400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr4:48559800-48604400	Weak transcription	HepG2	liver
12	chr4:48561400-48604400	Weak transcription	Stomach Mucosa	stomach
13	chr4:48562600-48596600	Weak transcription	Fetal Brain Male	brain
14	chr4:48562800-48623200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr4:48563000-48637400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr4:48563400-48593600	Weak transcription	Spleen	Spleen
17	chr4:48573200-48604600	Weak transcription	NHLF	lung
18	chr4:48573200-48605600	Weak transcription	Pancreas	Pancrea
19	chr4:48573200-48605600	Weak transcription	Small Intestine	intestine
20	chr4:48575200-48643000	Weak transcription	HSMMtube	muscle
21	chr4:48578000-48596400	Weak transcription	Osteobl	bone
22	chr4:48578200-48605600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr4:48578600-48637000	Weak transcription	Esophagus	oesophagus
24	chr4:48579600-48615800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr4:48580200-48593800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr4:48582200-48594400	Strong transcription	Dnd41	blood
27	chr4:48582400-48593800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr4:48582400-48594400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr4:48583200-48593200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr4:48585000-48593000	Weak transcription	Fetal Heart	heart
31	chr4:48586000-48602200	Weak transcription	Fetal Intestine Small	intestine
32	chr4:48587000-48596800	Weak transcription	NHDF-Ad	bronchial
33	chr4:48587400-48604600	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr4:48587600-48593800	Strong transcription	HMEC	breast
35	chr4:48587800-48593400	Weak transcription	Psoas Muscle	Psoas
36	chr4:48588000-48593400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr4:48588400-48596200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr4:48588400-48602600	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr4:48588400-48644600	Weak transcription	Colon Smooth Muscle	Colon
40	chr4:48588800-48593200	Weak transcription	Primary hematopoietic stem cells	blood
41	chr4:48588800-48596800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr4:48588800-48597000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr4:48588800-48619600	Weak transcription	Rectal Smooth Muscle	rectum
44	chr4:48589800-48593400	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr4:48589800-48593800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr4:48589800-48593800	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr4:48589800-48594000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr4:48589800-48594000	Strong transcription	Primary T cells from cord blood	blood
49	chr4:48589800-48594000	Strong transcription	Duodenum Mucosa	Duodenum
50	chr4:48589800-48594000	Strong transcription	Fetal Thymus	thymus

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