Variant report

Variant	rs6548601
Chromosome Location	chr3:78990607-78990608
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr3:78990564-78991163	MCF10A-Er-Src	breast:	n/a	n/a
2	KAP1	chr3:78990605-78991152	U2OS	brain:	n/a	n/a
3	RCOR1	chr3:78990353-78991709	IMR90	lung:	n/a	n/a
4	FOS	chr3:78990390-78991169	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr3:78990499-78991169	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
RN7SL751P	TF binding region

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs13075210	0.92[CHB][hapmap];0.83[EUR][1000 genomes]
rs1487135	0.81[CHB][hapmap]
rs162262	0.86[CHB][hapmap]
rs162263	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs162264	0.91[CEU][hapmap];0.94[CHB][hapmap]
rs162265	0.86[CEU][hapmap];0.92[CHB][hapmap];0.82[EUR][1000 genomes]
rs162268	0.96[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs162423	0.81[CHB][hapmap]
rs162425	0.81[CEU][hapmap];0.84[CHB][hapmap]
rs162427	0.82[CHB][hapmap]
rs162428	0.94[CHB][hapmap]
rs162429	0.93[CHB][hapmap]
rs17313732	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs1825760	0.81[CHB][hapmap]
rs186688	0.92[CEU][hapmap];0.94[CHB][hapmap]
rs2018432	0.81[CHB][hapmap]
rs2082973	0.81[CHB][hapmap]
rs328045	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs328047	0.96[CEU][hapmap];1.00[CHB][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs329805	0.94[CHB][hapmap]
rs329813	0.86[CHB][hapmap]
rs329814	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs329816	0.88[CEU][hapmap];0.94[CHB][hapmap]
rs329819	0.84[CEU][hapmap];0.93[CHB][hapmap]
rs329822	1.00[CHB][hapmap]
rs329825	0.91[CEU][hapmap];0.92[CHB][hapmap]
rs331158	0.86[CHB][hapmap]
rs331199	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs369346	0.92[CEU][hapmap];0.94[CHB][hapmap];0.82[EUR][1000 genomes]
rs379346	0.91[CEU][hapmap];0.93[CHB][hapmap];0.82[EUR][1000 genomes]
rs387900	0.96[CEU][hapmap];0.94[CHB][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs388421	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs420481	0.80[EUR][1000 genomes]
rs425121	0.82[EUR][1000 genomes]
rs434929	0.82[EUR][1000 genomes]
rs4681013	0.85[CHB][hapmap]
rs479956	0.87[CEU][hapmap];0.94[CHB][hapmap];0.82[EUR][1000 genomes]
rs484531	0.82[EUR][1000 genomes]
rs498805	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs512135	0.82[EUR][1000 genomes]
rs531125	0.81[CHB][hapmap]
rs6772919	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6800782	0.83[CEU][hapmap];0.94[CHB][hapmap]
rs7610996	0.81[CHB][hapmap]
rs7617538	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs7619765	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010804	chr3:78739648-79087470	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv533681	chr3:78750924-79017336	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv834744	chr3:78911545-79076470	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv966945	chr3:78990076-78992480	Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78963200-78991000	Weak transcription	Fetal Brain Male	brain
2	chr3:78967200-79000600	Weak transcription	Fetal Kidney	kidney
3	chr3:78969000-78990800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:78969000-78991000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:78969600-79000600	Weak transcription	HepG2	liver
6	chr3:78970400-78991000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:78977200-78990800	Weak transcription	Psoas Muscle	Psoas
8	chr3:78978400-78992200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:78978800-78990800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr3:78981600-78991600	Weak transcription	Fetal Heart	heart
11	chr3:78982400-79001800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr3:78986000-78990800	Weak transcription	NHLF	lung
13	chr3:78986200-78990800	Weak transcription	Primary T cells from cord blood	blood
14	chr3:78986800-78992200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:78988000-78991000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr3:78988000-78993600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr3:78988000-79002400	Weak transcription	Aorta	Aorta
18	chr3:78988200-78990800	Weak transcription	Fetal Stomach	stomach
19	chr3:78988200-78992800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr3:78988400-78990800	Weak transcription	Fetal Lung	lung
21	chr3:78988400-78991200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:78988400-78991400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:78988400-78992400	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr3:78989200-78991000	Enhancers	Colon Smooth Muscle	Colon
25	chr3:78989600-78991000	Enhancers	Rectal Smooth Muscle	rectum
26	chr3:78989600-78991600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:78990000-78991600	Enhancers	Muscle Satellite Cultured Cells	--
28	chr3:78990200-78991400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:78990200-78991600	Enhancers	Osteobl	bone
30	chr3:78990400-78991400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:78990400-78991400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:78990400-78991400	Enhancers	NHDF-Ad	bronchial
33	chr3:78990400-78991600	Enhancers	NHEK	skin
34	chr3:78990400-78992000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr3:78990600-78991600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr3:78990600-78991600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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