Variant report

Variant	rs6469994
Chromosome Location	chr8:122175814-122175815
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:122174198..122176101-chr8:122438175..122440772,2	MCF-7	breast:
2	chr8:122166497..122169768-chr8:122175078..122179332,4	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10100190	0.94[ASN][1000 genomes]
rs10101113	0.99[ASN][1000 genomes]
rs10109367	0.98[ASN][1000 genomes]
rs10109502	0.96[ASN][1000 genomes]
rs10109711	0.93[ASN][1000 genomes]
rs10956005	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11997916	0.96[ASN][1000 genomes]
rs12547780	0.94[ASN][1000 genomes]
rs12681217	0.94[ASN][1000 genomes]
rs12681237	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12682637	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13252222	0.97[ASN][1000 genomes]
rs13262055	0.97[ASN][1000 genomes]
rs1368594	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1368595	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1368605	0.94[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.84[MEX][hapmap];0.94[MKK][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1433392	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1504638	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1821323	0.99[ASN][1000 genomes]
rs1836070	0.94[ASN][1000 genomes]
rs2019363	0.82[EUR][1000 genomes]
rs2082534	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2134932	0.94[ASN][1000 genomes]
rs2134933	0.94[ASN][1000 genomes]
rs2202382	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2202383	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2386265	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2386266	0.98[ASN][1000 genomes]
rs28738104	0.94[ASN][1000 genomes]
rs2891977	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34173371	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35517836	0.86[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs35627384	0.93[ASN][1000 genomes]
rs4145811	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4282580	1.00[ASN][1000 genomes]
rs4424262	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4560798	0.98[ASN][1000 genomes]
rs4610754	0.94[ASN][1000 genomes]
rs4870759	0.98[ASN][1000 genomes]
rs4870760	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4870761	0.99[ASN][1000 genomes]
rs4871163	0.92[ASN][1000 genomes]
rs4871164	0.94[ASN][1000 genomes]
rs4871165	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4871166	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4871167	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4871169	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61074667	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67731008	0.81[EUR][1000 genomes]
rs6997513	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7016750	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7016899	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7017023	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7017048	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7357563	0.97[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	nsv465790	chr8:121853405-122185415	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv612114	chr8:121853405-122185415	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv891424	chr8:121873345-122393258	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	esv1844734	chr8:121928250-122283585	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv3330574	chr8:122039099-122386130	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv891426	chr8:122078334-122393258	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1021839	chr8:122173682-122240824	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6469994	NSMCE2	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:122167800-122176200	Weak transcription	Stomach Mucosa	stomach
2	chr8:122168000-122176800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr8:122168400-122176200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr8:122171000-122176400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr8:122173200-122177200	Enhancers	NHDF-Ad	bronchial
6	chr8:122174200-122176000	Enhancers	Hela-S3	cervix
7	chr8:122174200-122177200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr8:122174200-122177800	Enhancers	HMEC	breast
9	chr8:122174400-122176000	Enhancers	A549	lung
10	chr8:122174400-122177400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr8:122174400-122177800	Enhancers	NH-A	brain
12	chr8:122174400-122178800	Enhancers	Fetal Lung	lung
13	chr8:122174600-122176200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr8:122174600-122176800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr8:122174600-122176800	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr8:122174600-122176800	Enhancers	Fetal Intestine Large	intestine
17	chr8:122174600-122177600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr8:122174600-122177800	Enhancers	HSMMtube	muscle
19	chr8:122174800-122176800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr8:122174800-122177600	Weak transcription	HUVEC	blood vessel
21	chr8:122175000-122176000	Weak transcription	NHEK	skin
22	chr8:122175400-122176000	Enhancers	Fetal Stomach	stomach
23	chr8:122175400-122177000	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr8:122175400-122177000	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr8:122175400-122177200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr8:122175400-122177200	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr8:122175400-122178800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr8:122175600-122176000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr8:122175600-122176400	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr8:122175600-122176600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr8:122175800-122176000	Flanking Active TSS	HSMM	muscle
32	chr8:122175800-122176000	Flanking Active TSS	Osteobl	bone
33	chr8:122175800-122176400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr8:122175800-122176600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr8:122175800-122176800	Enhancers	Fetal Intestine Small	intestine
36	chr8:122175800-122176800	Enhancers	Fetal Muscle Leg	muscle
37	chr8:122175800-122176800	Enhancers	HepG2	liver
38	chr8:122175800-122176800	Enhancers	Monocytes-CD14+_RO01746	blood
39	chr8:122175800-122177000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
40	chr8:122175800-122177200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr8:122175800-122177200	Enhancers	Adipose Nuclei	Adipose
42	chr8:122175800-122177200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr8:122175800-122177800	Enhancers	Placenta	Placenta
44	chr8:122175800-122177800	Enhancers	NHLF	lung
45	chr8:122175800-122178000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr8:122175800-122178000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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