Variant report

Variant	rs11987297
Chromosome Location	chr8:99938470-99938471
allele	C/T
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	TCF12	chr8:99937787-99938621	SK-N-SH	brain:	n/a	chr8:99938435-99938445
2	GATA2	chr8:99937860-99938534	SH-SY5Y	brain:	n/a	chr8:99938416-99938425 chr8:99938509-99938518 chr8:99938413-99938429 chr8:99938274-99938284
3	GATA3	chr8:99937645-99938670	SK-N-SH	brain:	n/a	chr8:99938416-99938425 chr8:99938509-99938518 chr8:99938413-99938429 chr8:99938598-99938605 chr8:99938274-99938284
4	PBX3	chr8:99937853-99938602	SK-N-SH	brain:	n/a	n/a
5	GATA3	chr8:99937887-99938615	SK-N-SH	brain:	n/a	chr8:99938416-99938425 chr8:99938509-99938518 chr8:99938413-99938429 chr8:99938598-99938605 chr8:99938274-99938284
6	NFIC	chr8:99937834-99938577	SK-N-SH	brain:	n/a	n/a
7	TCF12	chr8:99937711-99938631	SK-N-SH	brain:	n/a	chr8:99938435-99938445
8	POLR2A	chr8:99938069-99938486	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:120635323..120636844-chr8:99936568..99939142,2	MCF-7	breast:
2	chr8:99937897..99939994-chr8:99955043..99958506,3	K562	blood:
3	chr8:99836376..99837915-chr8:99938345..99940401,2	MCF-7	breast:
4	chr8:99936963..99939745-chr8:99942656..99945387,2	MCF-7	breast:
5	chr8:99931677..99933733-chr8:99937087..99939527,3	MCF-7	breast:
6	chr8:99933065..99935408-chr8:99936825..99939811,2	MCF-7	breast:

Variant related genes	Relation type
RN7SKP85	TF binding region
ENSG00000164920	Chromatin interaction
ENSG00000089157	Chromatin interaction
ENSG00000104375	Chromatin interaction
ENSG00000271930	Chromatin interaction
ENSG00000223281	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10504987	0.94[GIH][hapmap]
rs11985354	0.86[ASN][1000 genomes]
rs11985377	0.86[ASN][1000 genomes]
rs11986449	0.83[ASW][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.90[LWK][hapmap];0.90[YRI][hapmap];0.91[ASN][1000 genomes]
rs11987308	0.90[CHB][hapmap];0.91[ASN][1000 genomes]
rs11987800	0.91[ASN][1000 genomes]
rs11988364	0.91[ASN][1000 genomes]
rs11989082	1.00[ASW][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.97[LWK][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11989805	0.97[ASN][1000 genomes]
rs11990131	0.97[ASN][1000 genomes]
rs11990888	0.86[ASN][1000 genomes]
rs11993237	0.86[ASN][1000 genomes]
rs11995021	0.86[ASN][1000 genomes]
rs11995381	0.97[ASN][1000 genomes]
rs11996944	0.86[ASN][1000 genomes]
rs11997079	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11997104	0.86[ASN][1000 genomes]
rs11998168	0.91[ASN][1000 genomes]
rs11998193	0.90[CHB][hapmap];0.87[CHD][hapmap];0.81[LWK][hapmap];0.85[YRI][hapmap];0.86[ASN][1000 genomes]
rs11998245	0.90[CHB][hapmap];0.90[YRI][hapmap];0.86[ASN][1000 genomes]
rs1447244	0.90[CHB][hapmap];0.85[YRI][hapmap];0.97[ASN][1000 genomes]
rs16897132	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17374005	0.94[GIH][hapmap]
rs35082816	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35318343	0.91[ASN][1000 genomes]
rs4501558	0.90[CHB][hapmap];0.86[ASN][1000 genomes]
rs4585717	0.97[ASN][1000 genomes]
rs4734422	0.97[ASN][1000 genomes]
rs4734423	0.97[ASN][1000 genomes]
rs4735586	0.90[CHB][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4735587	0.97[ASN][1000 genomes]
rs4735588	0.90[CHB][hapmap];0.97[ASN][1000 genomes]
rs4735590	0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4735593	0.97[ASN][1000 genomes]
rs4735594	0.97[ASN][1000 genomes]
rs4735595	0.91[ASN][1000 genomes]
rs4735596	0.91[ASN][1000 genomes]
rs4735598	0.90[CHB][hapmap];0.90[YRI][hapmap];0.91[ASN][1000 genomes]
rs4735605	0.86[ASN][1000 genomes]
rs57231976	0.91[ASN][1000 genomes]
rs72672316	0.86[ASN][1000 genomes]
rs745721	0.97[ASN][1000 genomes]
rs7814088	0.90[CHB][hapmap];0.87[CHD][hapmap];0.81[LWK][hapmap];0.85[YRI][hapmap];0.97[ASN][1000 genomes]
rs7814120	0.97[ASN][1000 genomes]
rs7814617	0.97[ASN][1000 genomes]
rs7818738	0.86[ASN][1000 genomes]
rs7819606	0.86[ASN][1000 genomes]
rs7820829	0.94[GIH][hapmap]
rs7829389	0.82[CHB][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7832595	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027025	chr8:99672977-100115315	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv539690	chr8:99672977-100115315	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv1031089	chr8:99715785-100399935	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv1023227	chr8:99902615-100290948	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv539692	chr8:99902615-100290948	ZNF genes & repeats Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv6327	chr8:99919634-99964563	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	esv1803951	chr8:99922754-100191783	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv611809	chr8:99925628-100093510	Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv531505	chr8:99932947-100464147	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
10	nsv515049	chr8:99934848-99938584	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11987297	RRM2B	cis	cerebellum	SCAN
rs11987297	NACAP1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:99927200-99942000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr8:99933200-99939000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr8:99934800-99938800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr8:99934800-99938800	Weak transcription	NHEK	skin
5	chr8:99935000-99938800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr8:99935000-99939000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr8:99935600-99939800	Enhancers	Fetal Lung	lung
8	chr8:99935800-99939800	Enhancers	Ovary	ovary
9	chr8:99936400-99939400	Enhancers	Fetal Stomach	stomach
10	chr8:99936800-99939400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr8:99936800-99939800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr8:99937000-99946000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr8:99937200-99940800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr8:99937400-99938600	Enhancers	Osteobl	bone
15	chr8:99937600-99939000	Enhancers	Fetal Kidney	kidney
16	chr8:99937600-99940600	Enhancers	NHDF-Ad	bronchial
17	chr8:99938000-99939000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr8:99938000-99939200	Enhancers	Fetal Muscle Leg	muscle
19	chr8:99938000-99940600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr8:99938200-99939200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr8:99938200-99944600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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