Variant report

Variant	rs7517539
Chromosome Location	chr1:93434725-93434726
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:93425058..93429733-chr1:93431759..93435608,8	K562	blood:
2	chr1:93425993..93428373-chr1:93433568..93436256,2	MCF-7	breast:
3	chr1:93433953..93434929-chr1:93527495..93528205,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000154511	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1011663	0.93[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs10747454	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11164850	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11164851	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11164854	0.94[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12049007	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12120036	0.90[ASN][1000 genomes]
rs12130044	0.94[CEU][hapmap];0.93[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs12133990	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12144226	0.93[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1415069	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1678784	0.84[ASN][1000 genomes]
rs2086314	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2127398	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2127400	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28561471	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3943283	0.94[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4515797	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4847226	0.89[ASN][1000 genomes]
rs4847389	0.85[ASN][1000 genomes]
rs514235	0.81[CHB][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs521428	0.81[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs534409	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs567613	0.81[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs594527	0.84[ASN][1000 genomes]
rs606344	0.84[ASN][1000 genomes]
rs619784	0.84[ASN][1000 genomes]
rs641462	0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs660870	0.81[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs663112	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6671078	0.88[ASN][1000 genomes]
rs6671268	0.81[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs6681429	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7524934	0.94[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs753391	0.85[ASN][1000 genomes]
rs770883	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs945630	0.89[EUR][1000 genomes];0.98[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7517539	FAM69A	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93428200-93438400	Weak transcription	Brain Angular Gyrus	brain
2	chr1:93428400-93435000	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr1:93428400-93438200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:93428400-93445800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr1:93428600-93436800	Weak transcription	NHEK	skin
6	chr1:93429200-93438200	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr1:93430200-93436600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:93431200-93437800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:93431600-93437600	Weak transcription	Dnd41	blood
10	chr1:93431600-93438600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr1:93431600-93438600	Weak transcription	Thymus	Thymus
12	chr1:93433200-93445000	Enhancers	Primary B cells from cord blood	blood
13	chr1:93433400-93436000	Enhancers	Monocytes-CD14+_RO01746	blood
14	chr1:93433600-93434800	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr1:93433600-93435000	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr1:93433600-93435200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:93433600-93435600	Enhancers	Primary T cells from cord blood	blood
18	chr1:93433600-93435800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:93433600-93436000	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr1:93433600-93439200	Enhancers	Fetal Heart	heart
21	chr1:93433800-93434800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr1:93433800-93438200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr1:93433800-93438200	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr1:93433800-93438200	Weak transcription	Placenta	Placenta
25	chr1:93434000-93437600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:93434000-93437600	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr1:93434000-93438000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr1:93434000-93438200	Weak transcription	Brain Substantia Nigra	brain
29	chr1:93434000-93439400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:93434200-93435800	Enhancers	GM12878-XiMat	blood
31	chr1:93434200-93436200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr1:93434200-93436600	Weak transcription	Fetal Intestine Small	intestine
33	chr1:93434200-93437800	Weak transcription	K562	blood
34	chr1:93434200-93438000	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr1:93434200-93438200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr1:93434200-93438200	Weak transcription	Brain Anterior Caudate	brain
37	chr1:93434200-93438200	Weak transcription	Brain Hippocampus Middle	brain
38	chr1:93434200-93438200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr1:93434200-93445600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr1:93434400-93435400	Weak transcription	Primary B cells from peripheral blood	blood
41	chr1:93434600-93435000	Weak transcription	Primary hematopoietic stem cells	blood
42	chr1:93434600-93437800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr1:93434600-93438000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr1:93434600-93438000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr1:93434600-93438000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr1:93434600-93438200	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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