Variant report

Variant	rs1478436
Chromosome Location	chr5:43288255-43288256
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:43284787-43292154	K562	blood:	n/a	n/a
2	POLR2A	chr5:43286213-43289153	K562	blood:	n/a	n/a
3	POLR2A	chr5:43284759-43289759	HepG2	liver:	n/a	n/a
4	POLR2A	chr5:43285561-43289251	HepG2	liver:	n/a	n/a
5	MBD4	chr5:43288214-43288990	HepG2	liver:	n/a	n/a
6	POLR2A	chr5:43284900-43292074	HepG2	liver:	n/a	n/a
7	POLR2A	chr5:43285520-43288419	HepG2	liver:	n/a	n/a
8	POLR2A	chr5:43286190-43289185	HepG2	liver:	n/a	n/a
9	POLR2A	chr5:43287293-43288581	GM12878	blood:	n/a	n/a
10	POLR2A	chr5:43285092-43289217	HepG2	liver:	n/a	n/a
11	CHD2	chr5:43287816-43289179	K562	blood:	n/a	n/a
12	POLR2A	chr5:43284491-43289202	GM12891	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:43065277..43067135-chr5:43287276..43290196,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC114947.1.1-1	chr5:43287703-43289827	ENSG00000261604.1
2	lnc-HMGCS1-1	chr5:43287801-43289456	NONHSAT101304

No data

Variant related genes	Relation type
ENSG00000261604	TF binding region
ENSG00000172262	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10037409	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10038859	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10040897	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10043148	0.86[EUR][1000 genomes]
rs10052384	0.86[EUR][1000 genomes]
rs10054415	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10056437	0.86[EUR][1000 genomes]
rs10062031	0.86[EUR][1000 genomes]
rs10062121	0.86[EUR][1000 genomes]
rs10062598	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10064967	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10067763	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10077324	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10079530	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10473306	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10473308	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11955467	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16874093	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16874094	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28450849	0.86[EUR][1000 genomes]
rs28608156	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28688522	0.85[AMR][1000 genomes]
rs28856961	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4326149	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55645370	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60520238	1.00[EUR][1000 genomes]
rs6865440	0.86[EUR][1000 genomes]
rs6884349	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6892413	0.86[EUR][1000 genomes]
rs6893898	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6894240	1.00[AFR][1000 genomes]
rs7356654	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7356727	0.87[AMR][1000 genomes]
rs73751075	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73751078	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73751082	0.86[EUR][1000 genomes]
rs73751083	0.86[EUR][1000 genomes]
rs7710717	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7715267	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7729140	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7729145	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7733732	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9292869	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9292870	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9292872	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9292875	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv508352	chr5:43237830-43391062	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43282800-43292800	Weak transcription	Hela-S3	cervix
2	chr5:43284200-43294000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:43284200-43309400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:43284800-43289000	Weak transcription	Small Intestine	intestine
5	chr5:43285000-43291400	Weak transcription	Fetal Intestine Small	intestine
6	chr5:43285000-43291400	Weak transcription	Osteobl	bone
7	chr5:43285000-43293400	Weak transcription	Pancreas	Pancrea
8	chr5:43285000-43300800	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr5:43285200-43294200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr5:43285400-43290400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr5:43285400-43291600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr5:43285400-43291600	Weak transcription	Fetal Kidney	kidney
13	chr5:43285400-43292000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr5:43285400-43292600	Weak transcription	Fetal Brain Male	brain
15	chr5:43285600-43290200	Weak transcription	Colon Smooth Muscle	Colon
16	chr5:43285600-43291600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr5:43285600-43293400	Weak transcription	Colonic Mucosa	Colon
18	chr5:43285600-43300000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr5:43285600-43302000	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr5:43285600-43302800	Strong transcription	Duodenum Mucosa	Duodenum
21	chr5:43285800-43289000	Strong transcription	Primary T cells from cord blood	blood
22	chr5:43285800-43291800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr5:43286200-43288400	Strong transcription	Brain Germinal Matrix	brain
24	chr5:43286200-43288800	Strong transcription	HSMM	muscle
25	chr5:43286200-43291600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr5:43286200-43295600	Strong transcription	HSMMtube	muscle
27	chr5:43286200-43298000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr5:43286200-43300600	Strong transcription	Fetal Intestine Large	intestine
29	chr5:43286400-43288800	Strong transcription	Adipose Nuclei	Adipose
30	chr5:43286400-43288800	Strong transcription	Fetal Muscle Leg	muscle
31	chr5:43286400-43289000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr5:43286400-43289200	Enhancers	Fetal Heart	heart
33	chr5:43286400-43289200	Strong transcription	Placenta	Placenta
34	chr5:43286400-43289600	Strong transcription	Fetal Brain Female	brain
35	chr5:43286400-43290400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr5:43286400-43290400	Weak transcription	Ovary	ovary
37	chr5:43286400-43291200	Strong transcription	NHLF	lung
38	chr5:43286400-43302200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr5:43286400-43302400	Strong transcription	GM12878-XiMat	blood
40	chr5:43286600-43288400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr5:43286600-43288800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr5:43286600-43288800	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr5:43286600-43291800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr5:43286600-43293200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr5:43286600-43293200	Strong transcription	Brain Substantia Nigra	brain
46	chr5:43286600-43296400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr5:43286600-43300400	Strong transcription	Fetal Thymus	thymus
48	chr5:43286600-43300800	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr5:43286600-43301000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr5:43286600-43301400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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