Variant report

Variant	rs641462
Chromosome Location	chr1:93458615-93458616
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:93426802..93428394-chr1:93457391..93459603,2	K562	blood:
2	chr1:93458427..93460268-chr1:93644070..93646479,2	K562	blood:
3	chr1:93458381..93461372-chr1:93479810..93482559,2	MCF-7	breast:
4	chr1:93317754..93320397-chr1:93457580..93459543,2	K562	blood:
5	chr1:93452194..93457760-chr1:93458258..93461631,4	K562	blood:
6	chr1:93304783..93306730-chr1:93457486..93459608,2	K562	blood:
7	chr1:93431361..93434358-chr1:93458613..93460256,2	K562	blood:
8	chr1:93323949..93325580-chr1:93458442..93460738,42	K562	blood:
9	chr1:93250962..93252670-chr1:93458393..93461376,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000154511	Chromatin interaction
ENSG00000117500	Chromatin interaction
ENSG00000207523	Chromatin interaction
ENSG00000122483	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1011663	0.85[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs10874752	0.89[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11164827	0.80[CHB][hapmap];0.87[JPT][hapmap]
rs11164838	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs11164848	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11164849	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11164850	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs11164851	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs11164854	0.85[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs12049007	0.90[ASN][1000 genomes]
rs12092304	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12120036	0.90[ASN][1000 genomes]
rs12130044	0.86[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs12144226	0.86[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs12747275	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1678784	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2086314	0.90[ASN][1000 genomes]
rs2127398	0.90[ASN][1000 genomes]
rs2127400	0.90[ASN][1000 genomes]
rs3943283	0.86[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs4515797	0.81[ASN][1000 genomes]
rs4847226	0.89[ASN][1000 genomes]
rs4847386	0.84[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4847389	1.00[CEU][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs514235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs521428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs534409	0.81[ASN][1000 genomes]
rs567613	1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs579800	0.82[EUR][1000 genomes]
rs594527	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs606344	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs619784	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs655026	0.80[EUR][1000 genomes]
rs660870	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs663112	0.88[ASN][1000 genomes]
rs6671078	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6671268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6681240	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6681345	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7517539	0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs7524934	0.85[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs753391	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs770883	0.86[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs770884	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]

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	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs641462	MTF2	cis	Skin Sun Exposed Lower leg	GTEx
rs641462	FAM69A	cis	Artery Tibial	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93451800-93466000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:93454400-93458800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr1:93454600-93458800	Enhancers	Primary T cells fromperipheralblood	blood
4	chr1:93454600-93459800	Enhancers	Primary T cells from cord blood	blood
5	chr1:93454600-93459800	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr1:93454800-93459800	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr1:93455400-93459800	Enhancers	Primary B cells from peripheral blood	blood
8	chr1:93456000-93461000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:93456200-93461200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:93456400-93459800	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr1:93456600-93459600	Weak transcription	Duodenum Mucosa	Duodenum
12	chr1:93456600-93459800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr1:93456600-93459800	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr1:93456600-93459800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr1:93457400-93459000	Weak transcription	Thymus	Thymus
16	chr1:93457400-93459200	Weak transcription	HepG2	liver
17	chr1:93457800-93459200	Weak transcription	Primary B cells from cord blood	blood
18	chr1:93457800-93459200	Weak transcription	K562	blood
19	chr1:93458000-93459000	Weak transcription	HSMM	muscle
20	chr1:93458000-93459800	Enhancers	Dnd41	blood
21	chr1:93458200-93459200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr1:93458200-93459200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr1:93458400-93459400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr1:93458600-93459800	Enhancers	HSMMtube	muscle

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