Variant report

Variant	rs7641727
Chromosome Location	chr3:119868575-119868576
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119811328..119819569-chr3:119859303..119870611,43	MCF-7	breast:
2	chr3:119854307..119856524-chr3:119867161..119869039,2	MCF-7	breast:
3	chr3:119867871..119870349-chr3:119875712..119877295,2	MCF-7	breast:
4	chr3:119809272..119819238-chr3:119861129..119869186,35	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242622	Chromatin interaction
ENSG00000082701	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10514764	0.91[CHB][hapmap];1.00[CHD][hapmap]
rs13073885	0.96[CEU][hapmap]
rs13095684	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3732362	0.86[CHB][hapmap]
rs4563433	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4676703	0.84[CEU][hapmap];0.81[AMR][1000 genomes]
rs4676811	0.96[CEU][hapmap]
rs4687895	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56148233	0.84[ASN][1000 genomes]
rs58043269	0.82[ASN][1000 genomes]
rs60845666	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6438565	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6776878	0.84[CEU][hapmap]
rs6781123	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6792814	0.84[CEU][hapmap]
rs6804257	0.82[CHD][hapmap];0.88[JPT][hapmap]
rs9844063	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9851098	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv829697	chr3:119802856-119918435	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
5	nsv877376	chr3:119824037-120119446	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv3967	chr3:119857708-119903115	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
7	nsv1013788	chr3:119866722-119912297	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7641727	KPNA1	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119864600-119871800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr3:119864800-119871600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr3:119865000-119870800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr3:119865000-119870800	Weak transcription	Osteobl	bone
5	chr3:119865200-119870200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:119865600-119868600	Enhancers	Thymus	Thymus
7	chr3:119865600-119868600	Enhancers	Dnd41	blood
8	chr3:119866600-119870800	Weak transcription	NHDF-Ad	bronchial
9	chr3:119866600-119871400	Weak transcription	Lung	lung
10	chr3:119866800-119871800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:119867000-119870800	Weak transcription	Stomach Mucosa	stomach
12	chr3:119867000-119872000	Weak transcription	Duodenum Mucosa	Duodenum
13	chr3:119867200-119869400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:119867200-119871800	Enhancers	NHEK	skin
15	chr3:119867200-119872000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr3:119867200-119873400	Weak transcription	HSMMtube	muscle
17	chr3:119867600-119869400	Weak transcription	Fetal Intestine Small	intestine
18	chr3:119867600-119871000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr3:119867600-119871400	Weak transcription	Spleen	Spleen
20	chr3:119867600-119872000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:119867800-119869400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:119867800-119870200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr3:119867800-119870400	Weak transcription	HepG2	liver
24	chr3:119867800-119870800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:119867800-119870800	Weak transcription	Placenta	Placenta
26	chr3:119867800-119870800	Weak transcription	Hela-S3	cervix
27	chr3:119867800-119870800	Weak transcription	HUVEC	blood vessel
28	chr3:119867800-119871000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:119867800-119871800	Weak transcription	Adipose Nuclei	Adipose
30	chr3:119867800-119871800	Weak transcription	Left Ventricle	heart
31	chr3:119868000-119870200	Weak transcription	Fetal Intestine Large	intestine
32	chr3:119868000-119870400	Weak transcription	HMEC	breast
33	chr3:119868400-119870600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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