Variant report

Variant	rs7559174
Chromosome Location	chr2:39364128-39364129
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39347118..39351165-chr2:39363686..39367178,4	MCF-7	breast:
2	chr2:39357363..39365432-chr2:39365480..39370907,10	K562	blood:
3	chr2:39350265..39353771-chr2:39361621..39365560,3	K562	blood:

Variant related genes	Relation type
ENSG00000115904	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10495883	1.00[GIH][hapmap];0.82[JPT][hapmap];0.81[LWK][hapmap]
rs13005167	0.84[AFR][1000 genomes]
rs17023241	0.82[JPT][hapmap]
rs17023272	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2373497	0.82[YRI][hapmap]
rs57362484	0.81[ASN][1000 genomes]
rs57866617	0.95[ASN][1000 genomes]
rs59340802	0.81[ASN][1000 genomes]
rs60718983	0.90[ASN][1000 genomes]
rs61392383	0.95[ASN][1000 genomes]
rs61456571	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6755453	0.81[ASN][1000 genomes]
rs72906433	0.81[ASN][1000 genomes]
rs72906442	0.81[ASN][1000 genomes]
rs72906449	0.81[ASN][1000 genomes]
rs72906454	0.81[ASN][1000 genomes]
rs72906466	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs72906469	0.81[ASN][1000 genomes]
rs72906483	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs72909647	0.88[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs72909674	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs72909679	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs72909693	0.95[ASN][1000 genomes]
rs7565814	0.82[JPT][hapmap]
rs7583010	0.82[JPT][hapmap]
rs7588123	0.81[ASN][1000 genomes]
rs7592176	0.81[ASN][1000 genomes]
rs7599990	0.82[JPT][hapmap]
rs7605889	0.81[ASN][1000 genomes]
rs7609455	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755359	chr2:39169049-39417849	Strong transcription Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv873885	chr2:39200198-39573521	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1010874	chr2:39255376-39604535	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv535649	chr2:39255376-39604535	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv531346	chr2:39263225-39606367	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv533348	chr2:39264345-39596169	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv1014520	chr2:39270598-39596299	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
8	nsv535650	chr2:39270598-39596299	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
9	nsv1009379	chr2:39271472-39604535	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
10	nsv581493	chr2:39277851-39547575	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
11	nsv581494	chr2:39277851-39626388	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
12	nsv533456	chr2:39281834-39596298	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
13	nsv581495	chr2:39282079-39475205	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7559174	SOS1	cis	lymphoblastoid	seeQTL
rs7559174	SOS1	cis	multi-tissue	Pritchard

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39352800-39368600	Weak transcription	HMEC	breast
2	chr2:39355400-39366000	Weak transcription	Hela-S3	cervix
3	chr2:39360600-39366800	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr2:39361000-39365000	Enhancers	Primary T cells fromperipheralblood	blood
5	chr2:39361800-39366800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr2:39361800-39366800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:39362400-39365800	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr2:39362600-39364200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr2:39362600-39364400	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr2:39362600-39364600	Enhancers	Fetal Thymus	thymus
11	chr2:39362600-39364600	Enhancers	Dnd41	blood
12	chr2:39362600-39364800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr2:39362600-39365400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr2:39362800-39364200	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr2:39362800-39364600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr2:39363200-39364800	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr2:39363200-39366800	Weak transcription	Fetal Intestine Large	intestine
18	chr2:39363200-39367000	Weak transcription	Primary B cells from cord blood	blood
19	chr2:39363200-39367400	Weak transcription	GM12878-XiMat	blood
20	chr2:39363400-39364800	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr2:39363400-39364800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr2:39363400-39365000	Weak transcription	HepG2	liver
23	chr2:39363400-39365400	Weak transcription	Aorta	Aorta
24	chr2:39363400-39366400	Weak transcription	K562	blood
25	chr2:39363400-39366800	Weak transcription	Primary B cells from peripheral blood	blood
26	chr2:39363600-39368800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr2:39363600-39371400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr2:39363800-39364200	Flanking Active TSS	Primary T cells from cord blood	blood
29	chr2:39364000-39364400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood

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