Variant report

Variant	rs6874848
Chromosome Location	chr5:118688115-118688116
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:118686914..118688782-chr5:118689065..118691768,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145779	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10077888	0.85[JPT][hapmap]
rs10478422	0.85[JPT][hapmap]
rs1155268	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1509141	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1509142	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1509144	0.86[JPT][hapmap]
rs1848554	0.95[JPT][hapmap]
rs192225	1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1995794	0.81[JPT][hapmap]
rs250298	0.80[CHB][hapmap]
rs250299	0.82[CHB][hapmap]
rs250302	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs250303	0.84[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs250304	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs32652	0.86[ASW][hapmap];0.86[CEU][hapmap];0.95[CHB][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs32654	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3813309	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs455991	0.80[JPT][hapmap]
rs4895369	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6595186	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7721752	0.85[JPT][hapmap]
rs924623	0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869828	chr5:118610548-118691190	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv599565	chr5:118661882-118691888	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv882775	chr5:118669094-118691888	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118670800-118691000	Weak transcription	Aorta	Aorta
2	chr5:118671200-118695400	Weak transcription	A549	lung
3	chr5:118674200-118689000	Weak transcription	Esophagus	oesophagus
4	chr5:118674400-118689000	Weak transcription	Gastric	stomach
5	chr5:118676800-118689000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr5:118676800-118691400	Weak transcription	Lung	lung
7	chr5:118678000-118690600	Weak transcription	NHEK	skin
8	chr5:118679000-118690600	Weak transcription	Fetal Intestine Small	intestine
9	chr5:118679000-118690800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr5:118679800-118689400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr5:118680200-118690400	Weak transcription	Stomach Mucosa	stomach
12	chr5:118680200-118690600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr5:118680200-118690600	Weak transcription	Colonic Mucosa	Colon
14	chr5:118680400-118689000	Weak transcription	Placenta	Placenta
15	chr5:118680400-118690600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr5:118680800-118691000	Weak transcription	HSMMtube	muscle
17	chr5:118682000-118689200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr5:118682000-118689200	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr5:118682000-118689200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr5:118682000-118689600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr5:118682200-118688200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr5:118682200-118689600	Weak transcription	Pancreas	Pancrea
23	chr5:118682600-118688200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr5:118682600-118689000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr5:118682600-118689400	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr5:118682600-118689600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr5:118682600-118690600	Weak transcription	Thymus	Thymus
28	chr5:118682600-118693600	Weak transcription	Dnd41	blood
29	chr5:118683000-118688200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr5:118683600-118689000	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr5:118683600-118689200	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr5:118683800-118689000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr5:118683800-118689800	Weak transcription	Primary hematopoietic stem cells	blood
34	chr5:118683800-118689800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr5:118684000-118688800	Weak transcription	Adipose Nuclei	Adipose
36	chr5:118684000-118688800	Weak transcription	Fetal Kidney	kidney
37	chr5:118684000-118690600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr5:118684000-118690800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr5:118684000-118691000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr5:118684000-118691000	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr5:118684000-118692800	Weak transcription	K562	blood
42	chr5:118684200-118689000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr5:118684200-118689000	Weak transcription	NHDF-Ad	bronchial
44	chr5:118684200-118689400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr5:118684200-118690400	Weak transcription	Hela-S3	cervix
46	chr5:118684200-118691000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr5:118684800-118689400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr5:118685000-118689000	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr5:118685000-118689000	Weak transcription	Duodenum Mucosa	Duodenum
50	chr5:118685000-118691000	Weak transcription	Sigmoid Colon	Sigmoid Colon

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