Variant report

Variant	rs549103
Chromosome Location	chr1:160715091-160715092
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:160714727..160717750-chr1:160718869..160722108,3	K562	blood:

Variant related genes	Relation type
ENSG00000026751	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs2295616	0.84[CHB][hapmap]
rs3766370	0.84[CHB][hapmap];0.86[CHD][hapmap]
rs489286	1.00[CHB][hapmap];0.82[CHD][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs495706	1.00[CHB][hapmap];0.82[CHD][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs518721	1.00[CHB][hapmap];0.82[CHD][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs573702	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][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	esv1822379	chr1:160545332-160831143	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv831714	chr1:160581168-160776809	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv428532	chr1:160671125-160767708	Flanking Active TSS Enhancers Genic enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs549103	SLAMF7	cis	lymphoblastoid	seeQTL
rs549103	LY9	Cis_1M	lymphoblastoid	RTeQTL
rs549103	CCT3	cis	parietal	SCAN
rs549103	SDHC	cis	parietal	SCAN
rs549103	SLAMF7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160708200-160715200	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr1:160709400-160718400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr1:160711200-160717200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr1:160711400-160715400	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr1:160711600-160715200	Enhancers	Fetal Thymus	thymus
6	chr1:160711600-160715200	Enhancers	Thymus	Thymus
7	chr1:160712000-160715400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr1:160712000-160716600	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr1:160712200-160716400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr1:160712800-160715200	Enhancers	Monocytes-CD14+_RO01746	blood
11	chr1:160712800-160718000	Enhancers	Primary T cells fromperipheralblood	blood
12	chr1:160713000-160720400	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr1:160713200-160715400	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr1:160713600-160718200	Weak transcription	Spleen	Spleen
15	chr1:160714000-160715800	Flanking Active TSS	GM12878-XiMat	blood
16	chr1:160714000-160717400	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr1:160714200-160716600	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr1:160714200-160717000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr1:160714400-160715200	Enhancers	Duodenum Mucosa	Duodenum
20	chr1:160714400-160718200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:160714400-160719800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr1:160714400-160726800	Weak transcription	Primary B cells from peripheral blood	blood
23	chr1:160714600-160715400	Enhancers	Primary T cells from cord blood	blood
24	chr1:160714800-160720800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr1:160715000-160715200	Enhancers	H1 Cell Line	embryonic stem cell
26	chr1:160715000-160715200	Enhancers	Colonic Mucosa	Colon
27	chr1:160715000-160715200	Enhancers	Lung	lung
28	chr1:160715000-160715400	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr1:160715000-160715600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:160715000-160715800	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr1:160715000-160717600	Enhancers	Primary T helper naive cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links