Variant report

Variant	rs2275583
Chromosome Location	chr10:99229394-99229395
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:99229192-99229717	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:99226678..99229676-chr10:99256675..99258497,3	K562	blood:

Variant related genes	Relation type
MMS19	TF binding region
ENSG00000155229	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10786350	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10786351	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs10882936	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10882937	0.93[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10882939	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10882940	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10882943	0.95[ASN][1000 genomes]
rs10882944	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10882946	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11189233	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11189238	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11189244	0.82[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap]
rs17112814	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs29001322	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4917772	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59554205	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7084687	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72833970	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7893335	0.91[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs7915501	0.91[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.82[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
rs2275583	RRP12	cis	cerebellum	SCAN
rs2275583	MMS19	cis	cerebellum	SCAN
rs2275583	RRP12	cis	parietal	SCAN
rs2275583	MMS19	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	chr10:99210000-99243800	Strong transcription	Primary T cells from cord blood	blood
3	chr10:99210000-99243800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr10:99210000-99244000	Strong transcription	Fetal Stomach	stomach
5	chr10:99210000-99244200	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr10:99210200-99243800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr10:99210400-99243600	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr10:99210400-99244800	Strong transcription	Fetal Thymus	thymus
9	chr10:99210600-99230800	Strong transcription	Fetal Brain Female	brain
10	chr10:99210600-99231600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr10:99210600-99234600	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr10:99210600-99238800	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr10:99210600-99239000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr10:99210600-99241800	Strong transcription	Thymus	Thymus
15	chr10:99210600-99243800	Strong transcription	Duodenum Mucosa	Duodenum
16	chr10:99210600-99244200	Strong transcription	Placenta	Placenta
17	chr10:99210800-99230800	Strong transcription	GM12878-XiMat	blood
18	chr10:99210800-99239000	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr10:99210800-99243800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr10:99210800-99244000	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr10:99210800-99246000	Strong transcription	Primary B cells from peripheral blood	blood
22	chr10:99211000-99230600	Strong transcription	Brain Germinal Matrix	brain
23	chr10:99211000-99231000	Strong transcription	H9 Cell Line	embryonic stem cell
24	chr10:99211000-99238800	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr10:99211000-99243800	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr10:99211000-99246400	Strong transcription	Dnd41	blood
27	chr10:99211200-99230800	Strong transcription	Brain Angular Gyrus	brain
28	chr10:99211200-99230800	Strong transcription	Brain Cingulate Gyrus	brain
29	chr10:99211200-99244800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr10:99211200-99246200	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr10:99211200-99246600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr10:99211400-99230800	Strong transcription	Primary B cells from cord blood	blood
33	chr10:99211400-99239000	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr10:99211400-99241600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr10:99211600-99230600	Strong transcription	Spleen	Spleen
36	chr10:99211600-99239000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr10:99211800-99230800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
38	chr10:99211800-99241200	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr10:99212000-99230800	Strong transcription	Rectal Smooth Muscle	rectum
40	chr10:99214000-99235600	Strong transcription	Brain Inferior Temporal Lobe	brain
41	chr10:99214200-99234400	Strong transcription	Lung	lung
42	chr10:99214400-99242000	Strong transcription	Fetal Muscle Trunk	muscle
43	chr10:99214400-99246400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr10:99214600-99242800	Strong transcription	Fetal Muscle Leg	muscle
45	chr10:99214600-99243800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr10:99214600-99243800	Strong transcription	Stomach Smooth Muscle	stomach
47	chr10:99214800-99243800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr10:99215000-99234600	Strong transcription	Colon Smooth Muscle	Colon
49	chr10:99215000-99238000	Strong transcription	Fetal Lung	lung
50	chr10:99215200-99230800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain

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