Variant report

Variant	rs13242539
Chromosome Location	chr7:7752559-7752560
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:7751274..7753371-chr7:7753426..7756190,2	K562	blood:
2	chr7:7604510..7607346-chr7:7752529..7754039,2	MCF-7	breast:
3	chr7:7749070..7751862-chr7:7752531..7755969,3	MCF-7	breast:
4	chr7:7713254..7715065-chr7:7752185..7753849,2	K562	blood:

Variant related genes	Relation type
ENSG00000164654	Chromatin interaction
ENSG00000272894	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1012997	0.90[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs10227168	0.87[ASN][1000 genomes]
rs10240471	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs10246966	0.87[ASN][1000 genomes]
rs10277292	1.00[CHB][hapmap];0.84[CHD][hapmap];0.87[ASN][1000 genomes]
rs10278708	0.86[ASN][1000 genomes]
rs11978146	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12111719	0.81[ASN][1000 genomes]
rs12702634	0.84[ASN][1000 genomes]
rs13231388	0.90[CHB][hapmap]
rs1544456	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1557997	0.90[CHB][hapmap]
rs17481971	0.89[CHB][hapmap];0.91[CHD][hapmap]
rs17482047	0.89[CHB][hapmap];0.87[CHD][hapmap]
rs2108000	0.90[CHB][hapmap]
rs28912669	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28912673	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35375940	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4313075	0.87[ASN][1000 genomes]
rs62432601	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67942668	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6944960	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs6947203	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs6966464	0.87[ASN][1000 genomes]
rs73352745	0.94[EUR][1000 genomes]
rs73352748	0.94[EUR][1000 genomes]
rs7781054	0.90[CHB][hapmap]
rs7800702	0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7800719	0.90[CHB][hapmap]
rs7800853	0.84[ASN][1000 genomes]
rs7804775	1.00[CHB][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	nsv606042	chr7:7427535-7876466	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats 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 miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv887477	chr7:7531819-7810122	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv1032670	chr7:7535515-8017077	Active TSS Weak transcription Enhancers Flanking Active TSS Strong 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 miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv8043	chr7:7589195-7862802	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv887478	chr7:7670718-7917360	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv887479	chr7:7681131-7779091	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv887480	chr7:7681131-7917360	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv887481	chr7:7681576-7779324	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv887482	chr7:7682439-7785047	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv887483	chr7:7682439-7798217	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv887484	chr7:7692483-7769363	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv887485	chr7:7692483-7917360	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
14	nsv606045	chr7:7704889-7755491	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	nsv887486	chr7:7712498-7785047	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
16	esv2752177	chr7:7729247-8177689	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
17	nsv1026564	chr7:7734846-7897847	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
18	nsv887487	chr7:7740914-7802561	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7737600-7778800	Weak transcription	Primary hematopoietic stem cells	blood
2	chr7:7740000-7759000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr7:7743600-7762800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr7:7743600-7772800	Weak transcription	Gastric	stomach
5	chr7:7745600-7758800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr7:7746000-7762400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr7:7747200-7753200	Weak transcription	GM12878-XiMat	blood
8	chr7:7747800-7763800	Weak transcription	Left Ventricle	heart
9	chr7:7748200-7772200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr7:7749200-7753400	Weak transcription	Fetal Thymus	thymus
11	chr7:7749200-7757200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr7:7749200-7758800	Weak transcription	Primary T cells from cord blood	blood
13	chr7:7749200-7770800	Weak transcription	Small Intestine	intestine
14	chr7:7749400-7754200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr7:7749400-7756000	Weak transcription	Fetal Intestine Small	intestine
16	chr7:7749600-7753400	Weak transcription	Brain Germinal Matrix	brain
17	chr7:7749800-7754000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr7:7750000-7754200	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr7:7750000-7754400	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr7:7750800-7760400	Weak transcription	Primary B cells from cord blood	blood
21	chr7:7751800-7754200	Enhancers	Dnd41	blood

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