Variant report

Variant	rs6451666
Chromosome Location	chr5:43069086-43069087
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD2	chr5:43068802-43069180	GM12878	blood:	n/a	n/a
2	CTCF	chr5:43068980-43069130	GM12870	blood:	n/a	n/a
3	ZBTB33	chr5:43068738-43069111	K562	blood:	n/a	n/a
4	ZBTB33	chr5:43068735-43069091	GM12878	blood:	n/a	n/a
5	CHD2	chr5:43068596-43069184	K562	blood:	n/a	n/a
6	EBF1	chr5:43068836-43069171	GM12878	blood:	n/a	n/a
7	BRCA1	chr5:43068811-43069145	GM12878	blood:	n/a	n/a
8	POLR2A	chr5:43068870-43069238	GM12878	blood:	n/a	n/a
9	POLR2A	chr5:43068809-43069208	GM12892	blood:	n/a	n/a
10	POLR2A	chr5:43068538-43069319	GM12892	blood:	n/a	n/a
11	POLR2A	chr5:43068828-43069242	GM12892	blood:	n/a	n/a
12	JUN	chr5:43063355-43069087	K562	blood:	n/a	chr5:43065126-43065140
13	POLR2A	chr5:43068826-43069310	GM12878	blood:	n/a	n/a
14	POLR2A	chr5:43068536-43069296	GM12892	blood:	n/a	n/a
15	ZBTB33	chr5:43068757-43069189	GM12878	blood:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:43062052..43069089-chr5:43119705..43123366,12	MCF-7	breast:
2	chr5:43064995..43071284-chr5:43119667..43123996,15	MCF-7	breast:
3	chr5:43037720..43044659-chr5:43062293..43069444,31	K562	blood:
4	chr5:43017018..43021813-chr5:43064660..43069370,12	MCF-7	breast:
5	chr5:43068379..43069957-chr5:43079642..43081288,2	K562	blood:
6	chr5:43038662..43048059-chr5:43059399..43070773,40	MCF-7	breast:
7	chr5:42907363..42912501-chr5:43064737..43069149,8	MCF-7	breast:
8	chr5:43067084..43070080-chr5:43601534..43603658,2	K562	blood:
9	chr5:43036901..43050217-chr5:43060442..43069391,53	MCF-7	breast:
10	chr5:43005189..43014948-chr5:43062554..43069130,17	MCF-7	breast:
11	chr5:43068783..43070775-chr5:43235999..43238082,2	K562	blood:
12	chr5:43015093..43022227-chr5:43063428..43069370,31	MCF-7	breast:
13	chr5:43060081..43061989-chr5:43067266..43069367,2	MCF-7	breast:
14	chr5:43065608..43069318-chr5:43481836..43485606,6	MCF-7	breast:
15	chr5:43034726..43053192-chr5:43061725..43074206,66	K562	blood:
16	chr5:43068548..43069734-chr5:43105535..43106442,4	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC114947.1.1-2	chr5:43067348-43069157	NONHSAT101283
2	lnc-C5orf39-1	chr5:43068623-43069159	NONHSAT101278

No data

Variant related genes	Relation type
ENSG00000177738	TF binding region
ENSG00000251131	Chromatin interaction
ENSG00000112992	Chromatin interaction
ENSG00000177738	Chromatin interaction
ENSG00000215068	Chromatin interaction
ENSG00000172262	Chromatin interaction
ENSG00000248092	Chromatin interaction
ENSG00000249492	Chromatin interaction
ENSG00000151881	Chromatin interaction
ENSG00000177721	Chromatin interaction
ENSG00000251656	Chromatin interaction
ENSG00000272144	Chromatin interaction
ENSG00000271788	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10051990	1.00[EUR][1000 genomes]
rs10052644	1.00[EUR][1000 genomes]
rs10054331	1.00[EUR][1000 genomes]
rs10056822	0.92[EUR][1000 genomes]
rs10064210	0.92[EUR][1000 genomes]
rs10071791	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10077219	0.84[EUR][1000 genomes]
rs1122510	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs13357786	1.00[EUR][1000 genomes]
rs13357845	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13360205	0.92[EUR][1000 genomes]
rs28490330	0.84[EUR][1000 genomes]
rs28573681	0.92[EUR][1000 genomes]
rs28609175	0.84[EUR][1000 genomes]
rs28628732	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56917209	0.92[EUR][1000 genomes]
rs585302	0.82[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs58980582	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60608708	0.92[EUR][1000 genomes]
rs6451670	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs673855	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6858989	1.00[EUR][1000 genomes]
rs6886503	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7709521	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7728625	0.87[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs9292865	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
2	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
3	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
4	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
5	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
6	nsv1024636	chr5:42959979-43295782	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
7	nsv537739	chr5:42959979-43295782	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
8	nsv870299	chr5:43053679-43107880	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43064600-43069200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr5:43064800-43069400	Active TSS	HSMM	muscle
3	chr5:43065800-43069600	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr5:43067200-43069200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr5:43067400-43069200	Flanking Active TSS	Primary hematopoietic stem cells	blood
6	chr5:43067400-43069200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr5:43067400-43069400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
8	chr5:43067400-43069400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
9	chr5:43067600-43069200	Flanking Active TSS	Brain Substantia Nigra	brain
10	chr5:43067600-43069400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
11	chr5:43067600-43069400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
12	chr5:43067600-43069600	Flanking Active TSS	Brain Hippocampus Middle	brain
13	chr5:43067800-43069200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr5:43067800-43069200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
15	chr5:43067800-43069400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
16	chr5:43067800-43069400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
17	chr5:43067800-43069400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr5:43067800-43069400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr5:43067800-43069400	Flanking Active TSS	HUVEC	blood vessel
20	chr5:43067800-43069600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr5:43067800-43069600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
22	chr5:43067800-43071200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr5:43068000-43069200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr5:43068000-43069200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr5:43068000-43069200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr5:43068000-43069200	Flanking Active TSS	Colon Smooth Muscle	Colon
27	chr5:43068000-43069200	Flanking Active TSS	Rectal Smooth Muscle	rectum
28	chr5:43068000-43069400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr5:43068000-43069400	Enhancers	Stomach Mucosa	stomach
30	chr5:43068000-43069400	Flanking Active TSS	Stomach Smooth Muscle	stomach
31	chr5:43068000-43069400	Flanking Active TSS	Osteobl	bone
32	chr5:43068000-43069800	Enhancers	Small Intestine	intestine
33	chr5:43068000-43070000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr5:43068000-43077600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr5:43068200-43069200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr5:43068200-43069200	Flanking Active TSS	HepG2	liver
37	chr5:43068200-43069200	Flanking Active TSS	HMEC	breast
38	chr5:43068200-43069400	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr5:43068200-43069400	Enhancers	Primary neutrophils fromperipheralblood	blood
40	chr5:43068200-43069600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr5:43068200-43069600	Enhancers	Primary B cells from peripheral blood	blood
42	chr5:43068200-43069600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
43	chr5:43068200-43069600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr5:43068200-43074200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr5:43068400-43069200	Flanking Active TSS	NHDF-Ad	bronchial
46	chr5:43068400-43069400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr5:43068400-43069400	Enhancers	Sigmoid Colon	Sigmoid Colon
48	chr5:43068400-43069600	Enhancers	Primary B cells from cord blood	blood
49	chr5:43068400-43069600	Genic enhancers	Placenta	Placenta
50	chr5:43068400-43069600	Enhancers	Spleen	Spleen

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