Variant report

Variant	rs2964200
Chromosome Location	chr5:57531438-57531439
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:57530338..57532834-chr5:57737218..57739511,2	MCF-7	breast:
2	chr5:57517523..57520170-chr5:57529878..57532281,2	MCF-7	breast:
3	chr5:57529817..57531823-chr5:57533642..57536408,2	K562	blood:

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1035475	1.00[CEU][hapmap]
rs10472035	0.88[CEU][hapmap]
rs10472036	0.88[CEU][hapmap]
rs10513142	0.81[AFR][1000 genomes]
rs13159047	1.00[YRI][hapmap]
rs13168414	1.00[ASW][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap]
rs1469090	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs151868	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs152010	1.00[YRI][hapmap]
rs154670	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs154671	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs154673	1.00[AFR][1000 genomes]
rs17709103	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs181745	1.00[ASW][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs1981838	1.00[ASW][hapmap];0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs2052547	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2081086	0.82[EUR][1000 genomes]
rs2081087	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2194195	0.80[EUR][1000 genomes]
rs2216678	0.84[AFR][1000 genomes]
rs2216679	0.88[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs2216685	0.80[EUR][1000 genomes]
rs2434584	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs245282	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs245285	1.00[ASW][hapmap];0.81[CHD][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs245287	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs245295	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs245296	0.84[AFR][1000 genomes]
rs245493	0.81[LWK][hapmap];1.00[YRI][hapmap]
rs246114	0.84[AFR][1000 genomes]
rs27210	0.81[AFR][1000 genomes]
rs27211	0.81[AFR][1000 genomes]
rs27840	0.81[AFR][1000 genomes]
rs2910569	0.88[CEU][hapmap]
rs2910573	1.00[YRI][hapmap]
rs2910577	1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2910592	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2910593	0.80[EUR][1000 genomes]
rs2910594	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs2910600	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs2910601	1.00[ASW][hapmap];0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs2910605	0.88[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs2910611	0.88[CEU][hapmap]
rs2964173	0.91[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2964184	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs2964193	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2964195	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2964205	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2964208	0.88[JPT][hapmap]
rs35263833	0.81[AFR][1000 genomes]
rs37484	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs37485	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs37486	1.00[AFR][1000 genomes]
rs37487	0.84[ASN][1000 genomes]
rs37488	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs37492	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs37516	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs37523	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs37526	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs37527	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs37528	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs37533	0.88[AFR][1000 genomes]
rs37536	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs40209	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs40210	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs41384	1.00[ASW][hapmap];0.81[CHD][hapmap];0.90[GIH][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs42963	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58174847	0.81[AFR][1000 genomes]
rs988697	0.80[EUR][1000 genomes]
rs989579	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432746	chr5:57502859-57547419	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2964200	NDUFAF2	cis	parietal	SCAN
rs2964200	BEND6	trans	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57521800-57535600	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr5:57525200-57535400	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr5:57526200-57535600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr5:57526200-57535600	Weak transcription	Psoas Muscle	Psoas
5	chr5:57526200-57544000	Weak transcription	Aorta	Aorta
6	chr5:57527200-57532600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr5:57527200-57535600	Weak transcription	HMEC	breast
8	chr5:57527400-57535800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr5:57530400-57532200	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr5:57530800-57531600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr5:57530800-57531600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr5:57530800-57532000	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr5:57531000-57531600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr5:57531000-57531600	Enhancers	Osteobl	bone
15	chr5:57531000-57531800	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr5:57531200-57531600	Enhancers	A549	lung
17	chr5:57531200-57531600	Enhancers	NHDF-Ad	bronchial
18	chr5:57531400-57534400	Weak transcription	Hela-S3	cervix
19	chr5:57531400-57535800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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