Variant report

Variant	rs6808017
Chromosome Location	chr3:50129969-50129970
allele	C/T
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	POLR2A	chr3:50129932-50129994	MCF-7	breast:	n/a	n/a
2	POLR2A	chr3:50129670-50130084	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:50125097..50128236-chr3:50128554..50131975,3	MCF-7	breast:
2	chr3:50129704..50131638-chr3:50149642..50152823,3	K562	blood:

Variant related genes	Relation type
RBM5	TF binding region
ENSG00000003756	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs2248256	1.00[AMR][1000 genomes]
rs59790389	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6787299	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72927506	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944416	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944438	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7620769	1.00[AMR][1000 genomes]
rs7636203	1.00[AMR][1000 genomes]
rs917019	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9756201	0.85[AFR][1000 genomes];1.00[AMR][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	nsv876767	chr3:49918751-50153356	Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv460527	chr3:50028385-50153356	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv590249	chr3:50028385-50153356	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv834690	chr3:50101835-50267584	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv515986	chr3:50104307-50267584	Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv432418	chr3:50114496-50224196	Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv1001775	chr3:50129479-50311666	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50127400-50132800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:50127400-50150000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:50127800-50130000	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr3:50127800-50157800	Strong transcription	H9 Cell Line	embryonic stem cell
5	chr3:50128000-50134600	Strong transcription	Esophagus	oesophagus
6	chr3:50128000-50152600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:50128000-50157800	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr3:50128000-50158000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr3:50128000-50158000	Strong transcription	Fetal Muscle Trunk	muscle
10	chr3:50128200-50130200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
11	chr3:50128200-50134600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
12	chr3:50128200-50135000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:50128200-50152800	Strong transcription	H1 Cell Line	embryonic stem cell
14	chr3:50128200-50158800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:50128400-50130000	Genic enhancers	Primary T cells fromperipheralblood	blood
16	chr3:50128400-50130800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr3:50128400-50132000	Strong transcription	Left Ventricle	heart
18	chr3:50128400-50148800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr3:50128400-50157800	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr3:50128400-50158200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:50128400-50158400	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr3:50128400-50159000	Strong transcription	Lung	lung
23	chr3:50128600-50130000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr3:50128600-50130000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
25	chr3:50128600-50130400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr3:50128600-50131000	Weak transcription	Psoas Muscle	Psoas
27	chr3:50128600-50131600	Strong transcription	K562	blood
28	chr3:50128600-50131800	Strong transcription	NHDF-Ad	bronchial
29	chr3:50128600-50132000	Strong transcription	Right Ventricle	heart
30	chr3:50128600-50132400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:50128600-50134600	Strong transcription	Aorta	Aorta
32	chr3:50128600-50137400	Weak transcription	Right Atrium	heart
33	chr3:50128600-50137400	Strong transcription	HSMM	muscle
34	chr3:50128600-50137400	Strong transcription	HSMMtube	muscle
35	chr3:50128600-50138000	Strong transcription	Small Intestine	intestine
36	chr3:50128600-50141600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr3:50128600-50148800	Strong transcription	Fetal Muscle Leg	muscle
38	chr3:50128600-50156200	Strong transcription	Ovary	ovary
39	chr3:50128600-50158000	Strong transcription	NH-A	brain
40	chr3:50128600-50158400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr3:50128600-50158400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr3:50128600-50158600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr3:50128600-50158600	Strong transcription	Colonic Mucosa	Colon
44	chr3:50128600-50158800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr3:50128600-50158800	Strong transcription	Brain Germinal Matrix	brain
46	chr3:50128600-50158800	Strong transcription	Placenta Amnion	Placenta Amnion
47	chr3:50128600-50159000	Strong transcription	Brain Angular Gyrus	brain
48	chr3:50128600-50159000	Strong transcription	Placenta	Placenta
49	chr3:50128600-50159000	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr3:50128600-50159200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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