Variant report

Variant	rs59271006
Chromosome Location	chr2:97529360-97529361
allele	A/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:3)
LncRNA
region (count:0)
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	chr2:97528950-97536892	K562	blood:	n/a	n/a
2	POLR2A	chr2:97528920-97537556	K562	blood:	n/a	n/a
3	POLR2A	chr2:97528923-97530407	K562	blood:	n/a	n/a
4	PML	chr2:97529128-97529502	K562	blood:	n/a	n/a
5	POLR2A	chr2:97529335-97529470	GM12878	blood:	n/a	n/a
6	POLR2A	chr2:97529149-97529706	GM12878	blood:	n/a	n/a
7	POLR2A	chr2:97526909-97536686	HepG2	liver:	n/a	n/a
8	POLR2A	chr2:97528980-97529479	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr2:97528940-97537661	K562	blood:	n/a	n/a
10	POLR2A	chr2:97529247-97529458	MCF-7	breast:	n/a	n/a
11	POLR2A	chr2:97528856-97529807	GM12878	blood:	n/a	n/a
12	POLR2A	chr2:97529281-97529438	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:97516728..97547486-chr2:97588377..97628331,265	MCF-7	breast:
2	chr2:97529274..97530551-chr2:97616477..97617259,4	MCF-7	breast:
3	chr2:97481636..97484312-chr2:97528160..97530681,3	MCF-7	breast:

No data

Variant related genes	Relation type
SEMA4C	TF binding region
ENSG00000168754	Chromatin interaction
ENSG00000168763	Chromatin interaction
ENSG00000252845	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11885652	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58446419	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62152867	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6758174	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7581764	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription 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	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv874680	chr2:97309574-97678319	Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
8	nsv526313	chr2:97333492-97660619	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
9	nsv874681	chr2:97410949-97577343	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
10	nsv874682	chr2:97423626-97567389	Transcr. at gene 5' and 3' Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97523800-97533000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:97524200-97533400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:97524400-97529600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr2:97524600-97530600	Weak transcription	Thymus	Thymus
5	chr2:97524600-97532800	Weak transcription	Hela-S3	cervix
6	chr2:97524600-97533400	Genic enhancers	Spleen	Spleen
7	chr2:97524600-97533600	Weak transcription	Psoas Muscle	Psoas
8	chr2:97524800-97529400	Enhancers	Primary hematopoietic stem cells	blood
9	chr2:97524800-97531600	Strong transcription	Esophagus	oesophagus
10	chr2:97525000-97531200	Weak transcription	HUVEC	blood vessel
11	chr2:97525000-97533800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr2:97525200-97531800	Weak transcription	Right Atrium	heart
13	chr2:97525400-97533600	Weak transcription	Small Intestine	intestine
14	chr2:97525600-97532400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr2:97525800-97530000	Strong transcription	Gastric	stomach
16	chr2:97525800-97530200	Genic enhancers	Brain Anterior Caudate	brain
17	chr2:97525800-97531000	Strong transcription	Muscle Satellite Cultured Cells	--
18	chr2:97525800-97531200	Strong transcription	Pancreas	Pancrea
19	chr2:97525800-97531200	Strong transcription	HSMMtube	muscle
20	chr2:97525800-97532000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:97525800-97532000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr2:97525800-97532000	Strong transcription	Osteobl	bone
23	chr2:97525800-97532200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr2:97525800-97532200	Strong transcription	Placenta Amnion	Placenta Amnion
25	chr2:97525800-97532400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr2:97525800-97532600	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr2:97525800-97532600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:97525800-97532600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr2:97525800-97532600	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr2:97525800-97532600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr2:97525800-97532600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr2:97525800-97532600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:97525800-97532600	Strong transcription	NHEK	skin
34	chr2:97525800-97532800	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr2:97525800-97533200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
36	chr2:97525800-97533200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr2:97525800-97533200	Strong transcription	Aorta	Aorta
38	chr2:97525800-97533400	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr2:97526000-97531400	Strong transcription	Fetal Brain Female	brain
40	chr2:97526000-97531800	Strong transcription	Brain Germinal Matrix	brain
41	chr2:97526000-97532600	Strong transcription	Ovary	ovary
42	chr2:97526000-97532800	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr2:97526000-97532800	Genic enhancers	Liver	Liver
44	chr2:97526200-97530800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr2:97526200-97531000	Strong transcription	NHLF	lung
46	chr2:97526200-97531800	Strong transcription	Adipose Nuclei	Adipose
47	chr2:97526200-97533000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr2:97526400-97530200	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr2:97526400-97530400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr2:97526400-97530400	Strong transcription	Lung	lung

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