Variant report

Variant	rs4241409
Chromosome Location	chr3:49496630-49496631
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49494808..49501210-chr3:49505386..49509341,14	MCF-7	breast:
2	chr3:49493044..49494602-chr3:49495069..49497320,2	K562	blood:
3	chr3:49452077..49454427-chr3:49496570..49500540,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173402	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs11130197	1.00[YRI][hapmap]
rs11130201	0.89[AFR][1000 genomes]
rs11708174	1.00[YRI][hapmap]
rs11717485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1522929	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1568663	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17080495	0.91[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17080510	0.91[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17080567	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17080664	0.92[YRI][hapmap];0.92[AFR][1000 genomes]
rs1996874	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2131107	0.89[AFR][1000 genomes]
rs2311794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2311801	0.91[YRI][hapmap];0.86[AFR][1000 genomes]
rs2329024	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs3870334	0.82[YRI][hapmap];0.86[AFR][1000 genomes]
rs3870340	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs3912831	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs4452334	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4855856	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs4855857	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs4855870	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4855872	0.90[AFR][1000 genomes]
rs4855874	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4855875	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4855876	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4855878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4855879	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55677747	0.81[AFR][1000 genomes]
rs55808753	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55990645	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56101322	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56760510	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56897974	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59579780	0.86[AFR][1000 genomes]
rs60011446	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61749312	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6446269	0.97[AFR][1000 genomes]
rs6446270	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6446271	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6446273	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6446276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6446278	0.89[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6446279	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6446280	0.92[AFR][1000 genomes]
rs6446281	0.84[AFR][1000 genomes]
rs6446282	0.86[AFR][1000 genomes]
rs6762593	1.00[YRI][hapmap]
rs6766297	1.00[AMR][1000 genomes]
rs6787665	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6793124	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6797164	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73830703	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73830704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73830705	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73830706	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831434	0.81[AFR][1000 genomes]
rs73831435	0.83[AFR][1000 genomes]
rs73831438	0.83[AFR][1000 genomes]
rs73831439	0.86[AFR][1000 genomes]
rs73831440	0.86[AFR][1000 genomes]
rs73831441	0.86[AFR][1000 genomes]
rs73831442	0.92[AFR][1000 genomes]
rs7646393	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs8179172	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9311441	1.00[AFR][1000 genomes]
rs9830627	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9861805	1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834687	chr3:49448632-49631788	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49482000-49498200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:49486600-49498600	Weak transcription	Duodenum Mucosa	Duodenum
3	chr3:49490600-49506600	Enhancers	Fetal Muscle Leg	muscle
4	chr3:49491800-49506200	Enhancers	Placenta	Placenta
5	chr3:49492600-49498000	Weak transcription	Stomach Mucosa	stomach
6	chr3:49492800-49498800	Weak transcription	Right Atrium	heart
7	chr3:49492800-49499200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr3:49493000-49498400	Weak transcription	Esophagus	oesophagus
9	chr3:49493200-49498600	Weak transcription	Spleen	Spleen
10	chr3:49493400-49498800	Weak transcription	Adipose Nuclei	Adipose
11	chr3:49493600-49497800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr3:49494000-49498600	Weak transcription	Left Ventricle	heart
13	chr3:49494000-49498800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr3:49494000-49498800	Weak transcription	Psoas Muscle	Psoas
15	chr3:49494200-49496800	Weak transcription	Fetal Heart	heart
16	chr3:49494200-49497800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:49494200-49497800	Weak transcription	HMEC	breast
18	chr3:49494200-49498200	Weak transcription	NHEK	skin
19	chr3:49494200-49498600	Weak transcription	NHLF	lung
20	chr3:49494200-49499000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:49494200-49499000	Weak transcription	Osteobl	bone
22	chr3:49494600-49501800	Enhancers	Fetal Muscle Trunk	muscle
23	chr3:49494800-49497800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:49494800-49498800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr3:49494800-49498800	Weak transcription	Right Ventricle	heart
26	chr3:49495000-49496800	Weak transcription	A549	lung
27	chr3:49495000-49498600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr3:49495000-49498800	Weak transcription	NHDF-Ad	bronchial
29	chr3:49496000-49500000	Enhancers	Muscle Satellite Cultured Cells	--
30	chr3:49496000-49501400	Enhancers	Pancreas	Pancrea
31	chr3:49496200-49497000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:49496200-49498000	Enhancers	Fetal Stomach	stomach
33	chr3:49496200-49498200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
34	chr3:49496200-49498200	Flanking Active TSS	HepG2	liver
35	chr3:49496200-49498400	Enhancers	Hela-S3	cervix
36	chr3:49496200-49499000	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr3:49496200-49499000	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr3:49496200-49499400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr3:49496200-49500000	Enhancers	H1 Cell Line	embryonic stem cell
40	chr3:49496200-49500000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:49496200-49500000	Enhancers	H9 Cell Line	embryonic stem cell
42	chr3:49496200-49500000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:49496200-49500000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr3:49496200-49500000	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr3:49496200-49500000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr3:49496200-49500000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr3:49496200-49500000	Enhancers	HSMM	muscle
48	chr3:49496200-49500000	Enhancers	HSMMtube	muscle
49	chr3:49496200-49500200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr3:49496200-49501200	Enhancers	ES-I3 Cell Line	embryonic stem cell

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