Variant report

Variant	rs10882939
Chromosome Location	chr10:99216432-99216433
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:99205739..99208326-chr10:99215340..99218229,2	K562	blood:
2	chr10:99205562..99208145-chr10:99216399..99218634,3	MCF-7	breast:
3	chr10:99214783..99216810-chr10:99219076..99220782,2	K562	blood:
4	chr10:99216173..99218492-chr10:99256425..99258366,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171307	Chromatin interaction
ENSG00000171311	Chromatin interaction
ENSG00000155229	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10786350	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10786351	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs10882936	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10882937	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10882940	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10882943	0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs10882944	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10882946	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11189233	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11189238	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11189244	0.86[CHB][hapmap];0.84[CHD][hapmap];0.80[JPT][hapmap]
rs17112814	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2275583	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]
rs29001322	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4917772	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59554205	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7084687	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72833970	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7893335	0.95[CHB][hapmap];0.86[CHD][hapmap]
rs7915501	0.95[CHB][hapmap];0.86[CHD][hapmap]

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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10882939	FRAT2	cis	multi-tissue	Pritchard
rs10882939	KIAA0690	cis	multi-tissue	Pritchard
rs10882939	RRP12	cis	parietal	SCAN
rs10882939	MMS19	cis	cerebellum	SCAN
rs10882939	FRAT1	cis	multi-tissue	Pritchard
rs10882939	RRP12	cis	cerebellum	SCAN
rs10882939	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	chr10:99207200-99216800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr10:99207400-99216600	Weak transcription	Small Intestine	intestine
4	chr10:99207400-99218600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr10:99207600-99218200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr10:99208000-99227000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr10:99208200-99216800	Weak transcription	Fetal Kidney	kidney
8	chr10:99208800-99216600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr10:99210000-99220400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr10:99210000-99223400	Strong transcription	NHLF	lung
11	chr10:99210000-99223600	Strong transcription	A549	lung
12	chr10:99210000-99228800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr10:99210000-99243800	Strong transcription	Primary T cells from cord blood	blood
14	chr10:99210000-99243800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr10:99210000-99244000	Strong transcription	Fetal Stomach	stomach
16	chr10:99210000-99244200	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr10:99210200-99223200	Strong transcription	HepG2	liver
18	chr10:99210200-99223600	Strong transcription	Fetal Intestine Small	intestine
19	chr10:99210200-99229200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr10:99210200-99243800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr10:99210400-99223200	Strong transcription	HSMM	muscle
22	chr10:99210400-99243600	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr10:99210400-99244800	Strong transcription	Fetal Thymus	thymus
24	chr10:99210600-99230800	Strong transcription	Fetal Brain Female	brain
25	chr10:99210600-99231600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr10:99210600-99234600	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr10:99210600-99238800	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr10:99210600-99239000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr10:99210600-99241800	Strong transcription	Thymus	Thymus
30	chr10:99210600-99243800	Strong transcription	Duodenum Mucosa	Duodenum
31	chr10:99210600-99244200	Strong transcription	Placenta	Placenta
32	chr10:99210800-99216600	Weak transcription	Psoas Muscle	Psoas
33	chr10:99210800-99230800	Strong transcription	GM12878-XiMat	blood
34	chr10:99210800-99239000	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr10:99210800-99243800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr10:99210800-99244000	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr10:99210800-99246000	Strong transcription	Primary B cells from peripheral blood	blood
38	chr10:99211000-99230600	Strong transcription	Brain Germinal Matrix	brain
39	chr10:99211000-99231000	Strong transcription	H9 Cell Line	embryonic stem cell
40	chr10:99211000-99238800	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr10:99211000-99243800	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr10:99211000-99246400	Strong transcription	Dnd41	blood
43	chr10:99211200-99223400	Strong transcription	Brain Substantia Nigra	brain
44	chr10:99211200-99230800	Strong transcription	Brain Angular Gyrus	brain
45	chr10:99211200-99230800	Strong transcription	Brain Cingulate Gyrus	brain
46	chr10:99211200-99244800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr10:99211200-99246200	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr10:99211200-99246600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr10:99211400-99223600	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr10:99211400-99230800	Strong transcription	Primary B cells from cord blood	blood

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