Variant report

Variant	rs2152092
Chromosome Location	chr10:99219885-99219886
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:25)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:25 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:99219782-99220074	HCT-116	colon:	n/a	n/a
2	POLR2A	chr10:99219812-99219923	A549	lung:	n/a	n/a
3	POLR2A	chr10:99219643-99220040	U87	brain:	n/a	n/a
4	POLR2A	chr10:99217959-99219911	K562	blood:	n/a	n/a
5	POLR2A	chr10:99219805-99220221	MCF-7	breast:	n/a	n/a
6	POLR2A	chr10:99217425-99222267	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr10:99217463-99220220	HepG2	liver:	n/a	n/a
8	POLR2A	chr10:99218880-99220737	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr10:99219632-99222536	HepG2	liver:	n/a	n/a
10	POLR2A	chr10:99217774-99219945	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr10:99217853-99219915	GM12891	blood:	n/a	n/a
12	POLR2A	chr10:99219601-99219945	A549	lung:	n/a	n/a
13	POLR2A	chr10:99217414-99222048	PFSK-1	brain:	n/a	n/a
14	POLR2A	chr10:99219036-99220248	K562	blood:	n/a	n/a
15	POLR2A	chr10:99219721-99219986	K562	blood:	n/a	n/a
16	POLR2A	chr10:99219725-99220580	HL-60	blood:	n/a	n/a
17	POLR2A	chr10:99219303-99220579	U87	brain:	n/a	n/a
18	POLR2A	chr10:99212148-99222485	K562	blood:	n/a	n/a
19	POLR2A	chr10:99219754-99219955	HepG2	liver:	n/a	n/a
20	POLR2A	chr10:99219753-99219916	GM12878	blood:	n/a	n/a
21	POLR2A	chr10:99219489-99221361	PANC-1	pancreas:	n/a	n/a
22	POLR2A	chr10:99217423-99222712	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr10:99219768-99219986	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr10:99219481-99219889	HepG2	liver:	n/a	n/a
25	POLR2A	chr10:99219133-99220927	U87	brain:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:99214783..99216810-chr10:99219076..99220782,2	K562	blood:
2	chr10:99210968..99213480-chr10:99218444..99221440,2	MCF-7	breast:

No data

Variant related genes	Relation type
MMS19	TF binding region
ENSG00000171307	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10786349	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10882938	0.82[CEU][hapmap];0.95[CHB][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10882941	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10882942	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11189240	0.81[EUR][1000 genomes]
rs11189245	0.81[CHB][hapmap]
rs12412017	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2007349	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2211243	0.80[ASN][1000 genomes]
rs2236575	0.96[CEU][hapmap];0.95[CHB][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3740526	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3818909	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4917773	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7068965	0.95[CHB][hapmap];0.88[CHD][hapmap];0.82[MEX][hapmap];0.80[ASN][1000 genomes]
rs7093946	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7096611	0.81[CHB][hapmap]
rs7897727	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7923913	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1817777	chr10:99196035-99558169	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2152092	C10orf131	cis	cerebellum	SCAN
rs2152092	MMS19	cis	cerebellum	SCAN
rs2152092	MMS19	cis	parietal	SCAN
rs2152092	RRP12	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99206800-99234200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr10:99208000-99227000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr10:99210000-99220400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr10:99210000-99223400	Strong transcription	NHLF	lung
5	chr10:99210000-99223600	Strong transcription	A549	lung
6	chr10:99210000-99228800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr10:99210000-99243800	Strong transcription	Primary T cells from cord blood	blood
8	chr10:99210000-99243800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr10:99210000-99244000	Strong transcription	Fetal Stomach	stomach
10	chr10:99210000-99244200	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr10:99210200-99223200	Strong transcription	HepG2	liver
12	chr10:99210200-99223600	Strong transcription	Fetal Intestine Small	intestine
13	chr10:99210200-99229200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr10:99210200-99243800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr10:99210400-99223200	Strong transcription	HSMM	muscle
16	chr10:99210400-99243600	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr10:99210400-99244800	Strong transcription	Fetal Thymus	thymus
18	chr10:99210600-99230800	Strong transcription	Fetal Brain Female	brain
19	chr10:99210600-99231600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr10:99210600-99234600	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr10:99210600-99238800	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr10:99210600-99239000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr10:99210600-99241800	Strong transcription	Thymus	Thymus
24	chr10:99210600-99243800	Strong transcription	Duodenum Mucosa	Duodenum
25	chr10:99210600-99244200	Strong transcription	Placenta	Placenta
26	chr10:99210800-99230800	Strong transcription	GM12878-XiMat	blood
27	chr10:99210800-99239000	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr10:99210800-99243800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr10:99210800-99244000	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr10:99210800-99246000	Strong transcription	Primary B cells from peripheral blood	blood
31	chr10:99211000-99230600	Strong transcription	Brain Germinal Matrix	brain
32	chr10:99211000-99231000	Strong transcription	H9 Cell Line	embryonic stem cell
33	chr10:99211000-99238800	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr10:99211000-99243800	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr10:99211000-99246400	Strong transcription	Dnd41	blood
36	chr10:99211200-99223400	Strong transcription	Brain Substantia Nigra	brain
37	chr10:99211200-99230800	Strong transcription	Brain Angular Gyrus	brain
38	chr10:99211200-99230800	Strong transcription	Brain Cingulate Gyrus	brain
39	chr10:99211200-99244800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr10:99211200-99246200	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr10:99211200-99246600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr10:99211400-99223600	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr10:99211400-99230800	Strong transcription	Primary B cells from cord blood	blood
44	chr10:99211400-99239000	Strong transcription	H1 Cell Line	embryonic stem cell
45	chr10:99211400-99241600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr10:99211600-99230600	Strong transcription	Spleen	Spleen
47	chr10:99211600-99239000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr10:99211800-99223400	Strong transcription	Brain Hippocampus Middle	brain
49	chr10:99211800-99223800	Strong transcription	Fetal Intestine Large	intestine
50	chr10:99211800-99230800	Strong transcription	iPS-15b Cell Line	embryonic stem cell

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