Variant report

Variant	rs10938521
Chromosome Location	chr4:48113219-48113220
allele	C/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	MAFK	chr4:48113073-48113223	K562	blood:	n/a	n/a
2	TCF7L2	chr4:48112895-48113407	HepG2	liver:	n/a	n/a
3	GATA3	chr4:48111371-48113231	SK-N-SH	brain:	n/a	chr4:48112406-48112422 chr4:48112897-48112904

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48107744..48110406-chr4:48112924..48114578,2	K562	blood:
2	chr4:48111744..48114510-chr4:48271581..48273231,2	MCF-7	breast:

Variant related genes	Relation type
RNU6-868P	TF binding region
ENSG00000200269	Chromatin interaction
ENSG00000135605	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10938519	0.82[MEX][hapmap]
rs11931912	0.83[CHD][hapmap];0.82[MEX][hapmap];1.00[YRI][hapmap]
rs11942098	0.84[AFR][1000 genomes]
rs12233700	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12646088	0.81[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap]
rs12647931	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs13151608	1.00[YRI][hapmap]
rs17655249	1.00[YRI][hapmap]
rs17655303	1.00[YRI][hapmap]
rs4446283	1.00[YRI][hapmap]
rs62298964	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62298965	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62298967	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs875179	0.90[CHB][hapmap];0.84[JPT][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	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10938521	NFXL1	cis	multi-tissue	Pritchard
rs10938521	TEC	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48103400-48114000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr4:48104400-48114000	Strong transcription	Primary T cells fromperipheralblood	blood
3	chr4:48106000-48115600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr4:48106000-48129400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr4:48106200-48114200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr4:48107400-48114400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr4:48109600-48113600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr4:48109600-48114800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr4:48109800-48115000	Strong transcription	Primary T cells from cord blood	blood
10	chr4:48110200-48114000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr4:48111400-48114200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr4:48111400-48114800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr4:48111600-48113600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr4:48111600-48114000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr4:48111600-48114600	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr4:48111600-48114800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr4:48111800-48113600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr4:48111800-48113600	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr4:48111800-48114000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr4:48111800-48114000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr4:48111800-48114000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr4:48111800-48114000	Weak transcription	NHEK	skin
23	chr4:48111800-48118600	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr4:48112000-48114000	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr4:48112200-48113600	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr4:48112200-48113600	Weak transcription	Osteobl	bone
27	chr4:48112200-48113800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr4:48112600-48113800	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr4:48112800-48114400	Transcr. at gene 5' and 3'	Primary Natural Killer cells fromperipheralblood	blood
30	chr4:48112800-48114600	Enhancers	HSMM	muscle
31	chr4:48113000-48114200	Enhancers	NH-A	brain
32	chr4:48113000-48115200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr4:48113200-48114200	Weak transcription	HSMMtube	muscle
34	chr4:48113200-48116800	Enhancers	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links