Variant report

Variant	rs6594302
Chromosome Location	chr5:107719162-107719163
allele	G/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	chr5:107716092-107719682	GM18505	blood:	n/a	n/a
2	POLR2A	chr5:107715759-107719979	GM12878	blood:	n/a	n/a
3	POLR2A	chr5:107716103-107719353	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr5:107716212-107719233	GM19193	blood:	n/a	n/a
5	POLR2A	chr5:107716204-107719676	Raji	blood:	n/a	n/a
6	POLR2A	chr5:107716068-107719494	GM12892	blood:	n/a	n/a
7	BCLAF1	chr5:107717545-107719214	GM12878	blood:	n/a	chr5:107717772-107717785 chr5:107717718-107717731 chr5:107717832-107717845 chr5:107718134-107718147 chr5:107717837-107717846 chr5:107717697-107717710 chr5:107717884-107717897
8	POLR2A	chr5:107716841-107719573	HepG2	liver:	n/a	n/a
9	POLR2A	chr5:107716150-107721128	MCF10A-Er-Src	breast:	n/a	n/a
10	MTA3	chr5:107716997-107719244	GM12878	blood:	n/a	n/a
11	POLR2A	chr5:107716786-107719225	GM12891	blood:	n/a	n/a
12	POLR2A	chr5:107715755-107719586	IMR90	lung:	n/a	n/a
13	MXI1	chr5:107716767-107719174	IMR90	lung:	n/a	n/a
14	POLR2A	chr5:107716923-107719184	K562	blood:	n/a	n/a
15	POLR2A	chr5:107715567-107721797	GM12891	blood:	n/a	n/a
16	POLR2A	chr5:107716752-107719409	GM12892	blood:	n/a	n/a
17	POLR2A	chr5:107715827-107719419	GM19099	blood:	n/a	n/a
18	POLR2A	chr5:107716891-107721217	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr5:107716862-107721767	K562	blood:	n/a	n/a
20	NFATC1	chr5:107717430-107719345	GM12878	blood:	n/a	n/a
21	POLR2A	chr5:107716924-107719494	PBDE	blood:	n/a	n/a
22	POLR2A	chr5:107715650-107720235	GM12878	blood:	n/a	n/a
23	POLR2A	chr5:107716342-107719183	K562	blood:	n/a	n/a
24	POLR2A	chr5:107717211-107719188	HepG2	liver:	n/a	n/a
25	CHD1	chr5:107715480-107719183	IMR90	lung:	n/a	chr5:107716684-107716694 chr5:107718041-107718051
26	POLR2A	chr5:107716125-107719271	GM18526	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:107717757..107719316-chr5:108082854..108085189,2	MCF-7	breast:
2	chr17:56707838..56709408-chr5:107717077..107719444,2	MCF-7	breast:
3	chr3:64105488..64107336-chr5:107718780..107720666,2	MCF-7	breast:
4	chr5:107703017..107709518-chr5:107714821..107720551,7	MCF-7	breast:
5	chr5:107673625..107675150-chr5:107717919..107720038,2	K562	blood:
6	chr5:107700359..107701872-chr5:107716648..107719223,2	MCF-7	breast:
7	chr5:107717243..107719303-chr5:108745580..108747696,2	MCF-7	breast:
8	chr5:107703047..107709148-chr5:107715421..107721287,10	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FER-2	chr5:107717801-107724211	NONHSAT103120

Variant related genes	Relation type
FBXL17	TF binding region
ENSG00000198961	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000151422	Chromatin interaction
ENSG00000145743	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11240963	1.00[EUR][1000 genomes]
rs55825519	1.00[EUR][1000 genomes]
rs56355836	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56929525	1.00[EUR][1000 genomes]
rs59704928	1.00[EUR][1000 genomes]
rs60042566	1.00[EUR][1000 genomes]
rs61614616	1.00[EUR][1000 genomes]
rs6862778	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6866453	1.00[MEX][hapmap]
rs6867893	1.00[EUR][1000 genomes]
rs6879616	0.86[ASW][hapmap];1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs73781332	1.00[EUR][1000 genomes]
rs73781333	1.00[EUR][1000 genomes]
rs73781335	1.00[EUR][1000 genomes]
rs73781336	1.00[EUR][1000 genomes]
rs73781339	1.00[EUR][1000 genomes]
rs73781340	1.00[EUR][1000 genomes]
rs73781341	1.00[EUR][1000 genomes]
rs73781344	1.00[EUR][1000 genomes]
rs73781345	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73781353	1.00[EUR][1000 genomes]
rs73781354	1.00[EUR][1000 genomes]
rs73781358	1.00[EUR][1000 genomes]
rs73781359	1.00[EUR][1000 genomes]
rs7706235	1.00[EUR][1000 genomes]
rs7713871	1.00[EUR][1000 genomes]
rs7722719	0.85[ASW][hapmap];1.00[MEX][hapmap]
rs7722938	0.85[ASW][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap]
rs7725340	1.00[EUR][1000 genomes]
rs7728430	1.00[MEX][hapmap]
rs7737226	1.00[EUR][1000 genomes]
rs962681	0.85[ASW][hapmap];1.00[MEX][hapmap]

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	nsv882683	chr5:107476501-107769095	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv882686	chr5:107564746-107769095	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv882689	chr5:107595383-108299744	Enhancers ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	esv2755544	chr5:107614101-107748101	Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:107715400-107719200	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr5:107716000-107719200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr5:107716000-107719400	Active TSS	Rectal Smooth Muscle	rectum
4	chr5:107718200-107719200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
5	chr5:107718200-107719200	Flanking Active TSS	Dnd41	blood
6	chr5:107718200-107719200	Flanking Active TSS	HMEC	breast
7	chr5:107718200-107719200	Flanking Active TSS	K562	blood
8	chr5:107718200-107719400	Flanking Active TSS	Primary hematopoietic stem cells	blood
9	chr5:107718200-107719400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
10	chr5:107718200-107719600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr5:107718200-107719800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr5:107718400-107719200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr5:107718400-107719200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
14	chr5:107718400-107719200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
15	chr5:107718400-107719200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
16	chr5:107718400-107719200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr5:107718400-107719200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr5:107718400-107719200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr5:107718400-107719200	Flanking Active TSS	A549	lung
20	chr5:107718400-107719200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr5:107718400-107719400	Flanking Active TSS	Primary B cells from cord blood	blood
22	chr5:107718400-107719400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr5:107718400-107719400	Flanking Active TSS	Fetal Heart	heart
24	chr5:107718600-107719200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr5:107718600-107719200	Flanking Active TSS	Primary B cells from peripheral blood	blood
26	chr5:107718600-107719200	Flanking Active TSS	Liver	Liver
27	chr5:107718600-107719200	Flanking Active TSS	Fetal Thymus	thymus
28	chr5:107718600-107719200	Flanking Active TSS	Stomach Mucosa	stomach
29	chr5:107718600-107719200	Enhancers	Spleen	Spleen
30	chr5:107718600-107719400	Flanking Active TSS	Primary T cells from cord blood	blood
31	chr5:107718600-107719400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr5:107718600-107719400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
33	chr5:107718600-107719400	Flanking Active TSS	GM12878-XiMat	blood
34	chr5:107718800-107719200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr5:107718800-107719200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr5:107718800-107719200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
37	chr5:107718800-107719200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
38	chr5:107718800-107719200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr5:107718800-107719200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr5:107718800-107719200	Active TSS	Brain Angular Gyrus	brain
41	chr5:107718800-107719200	Enhancers	Placenta	Placenta
42	chr5:107718800-107719200	Enhancers	Pancreas	Pancrea
43	chr5:107718800-107719200	Enhancers	Right Ventricle	heart
44	chr5:107718800-107719400	Enhancers	Placenta Amnion	Placenta Amnion
45	chr5:107718800-107719400	Enhancers	Hela-S3	cervix
46	chr5:107718800-107719400	Enhancers	NHLF	lung
47	chr5:107718800-107719600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr5:107718800-107719600	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr5:107718800-107720200	Weak transcription	HSMM	muscle
50	chr5:107718800-107731200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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