Variant report

Variant	rs16855510
Chromosome Location	chr2:10278878-10278879
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:26)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:26 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:10278567-10279995	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr2:10278421-10282354	U87	brain:	n/a	n/a
3	POLR2A	chr2:10278493-10279090	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr2:10278645-10278954	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr2:10274459-10280433	HepG2	liver:	n/a	n/a
6	POLR2A	chr2:10278867-10278923	ProgFib	skin:	n/a	n/a
7	POLR2A	chr2:10278555-10279178	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr2:10271895-10281381	U87	brain:	n/a	n/a
9	POLR2A	chr2:10275776-10279510	K562	blood:	n/a	n/a
10	POLR2A	chr2:10278656-10278907	MCF-7	breast:	n/a	n/a
11	POLR2A	chr2:10278569-10280077	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr2:10278571-10279005	U87	brain:	n/a	n/a
13	BCL3	chr2:10278551-10279088	A549	lung:	n/a	n/a
14	POLR2A	chr2:10278708-10278965	U87	brain:	n/a	n/a
15	POLR2A	chr2:10278426-10279046	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr2:10278564-10278945	A549	lung:	n/a	n/a
17	POLR2A	chr2:10278549-10279005	K562	blood:	n/a	n/a
18	POLR2A	chr2:10278665-10280059	K562	blood:	n/a	n/a
19	POLR2A	chr2:10278679-10280001	GM12878	blood:	n/a	n/a
20	POLR2A	chr2:10278585-10278960	HepG2	liver:	n/a	n/a
21	POLR2A	chr2:10278569-10279048	PFSK-1	brain:	n/a	n/a
22	POLR2A	chr2:10278580-10279896	K562	blood:	n/a	n/a
23	POLR2A	chr2:10278479-10280200	PANC-1	pancreas:	n/a	n/a
24	POLR2A	chr2:10278561-10279858	Raji	blood:	n/a	n/a
25	POLR2A	chr2:10278551-10278993	ECC-1	luminal epithelium:	n/a	n/a
26	POLR2A	chr2:10278724-10278924	Hela-S3	cervix:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:10278603..10281199-chr2:10574177..10576676,2	K562	blood:
2	chr2:10277705..10280483-chr2:10573985..10576380,2	MCF-7	breast:
3	chr2:10277542..10280020-chr2:10400338..10402509,2	MCF-7	breast:
4	chr2:10277738..10279513-chr2:10379719..10382264,2	K562	blood:
5	chr2:10217505..10219089-chr2:10278017..10279844,2	K562	blood:
6	chr2:10210334..10214416-chr2:10274346..10279304,5	K562	blood:
7	chr2:10262593..10265067-chr2:10276073..10279475,5	MCF-7	breast:
8	chr2:10217505..10219442-chr2:10278017..10279605,2	K562	blood:

No data

Variant related genes	Relation type
C2orf48	TF binding region
ENSG00000171848	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10172702	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10179663	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10179866	0.81[ASN][1000 genomes]
rs10192090	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10197121	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10202672	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10209383	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10754955	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11896140	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12692399	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12987867	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13009708	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13010608	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13028656	0.86[ASN][1000 genomes]
rs13398833	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13420725	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2110641	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2110642	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2160190	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2241113	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2357465	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2357466	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2357467	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4669531	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6432066	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6432067	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6432068	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6432069	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6432070	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6706570	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6707144	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6707406	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6709408	0.94[ASN][1000 genomes]
rs6715077	0.96[ASN][1000 genomes]
rs6749325	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6758411	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7420698	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7566175	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7605457	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011125	chr2:9996740-10293803	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv1011689	chr2:10023891-10293803	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv873634	chr2:10275814-10337034	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10263800-10283600	Weak transcription	Spleen	Spleen
2	chr2:10264200-10281800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:10265400-10280000	Weak transcription	Fetal Kidney	kidney
4	chr2:10265400-10284000	Weak transcription	Placenta	Placenta
5	chr2:10269600-10299400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:10269800-10285200	Weak transcription	Brain Germinal Matrix	brain
7	chr2:10271400-10303800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr2:10272200-10284000	Weak transcription	GM12878-XiMat	blood
9	chr2:10272600-10289800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr2:10273400-10285000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr2:10273600-10282400	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr2:10273600-10283400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:10273800-10281600	Weak transcription	Fetal Muscle Leg	muscle
14	chr2:10273800-10281800	Weak transcription	Duodenum Mucosa	Duodenum
15	chr2:10273800-10282000	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr2:10273800-10282600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr2:10273800-10282600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr2:10273800-10283200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr2:10273800-10283400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr2:10273800-10283400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr2:10273800-10289800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:10273800-10330400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr2:10274000-10282000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr2:10274000-10299200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:10275200-10284200	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr2:10275400-10281000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr2:10275400-10281400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr2:10276400-10279400	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr2:10276400-10307400	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr2:10276600-10281800	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr2:10276600-10284200	Weak transcription	NHLF	lung
32	chr2:10276600-10301800	Weak transcription	Osteobl	bone
33	chr2:10276800-10281600	Weak transcription	Fetal Stomach	stomach
34	chr2:10277000-10282000	Weak transcription	Fetal Intestine Small	intestine
35	chr2:10277200-10283400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr2:10277600-10280800	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr2:10277600-10281000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:10277600-10282800	Weak transcription	Fetal Intestine Large	intestine
39	chr2:10277600-10283400	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr2:10277600-10284000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr2:10277600-10321600	Weak transcription	K562	blood
42	chr2:10277800-10279200	Strong transcription	Dnd41	blood
43	chr2:10277800-10279400	Weak transcription	Fetal Thymus	thymus
44	chr2:10277800-10281000	Weak transcription	A549	lung
45	chr2:10277800-10281800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr2:10277800-10282000	Weak transcription	HepG2	liver
47	chr2:10277800-10295400	Weak transcription	Hela-S3	cervix
48	chr2:10278000-10281600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr2:10278000-10282000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr2:10278000-10282400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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