Variant report

Variant	rs11164850
Chromosome Location	chr1:93430926-93430927
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:93418758..93421387-chr1:93428230..93431121,2	MCF-7	breast:
2	chr1:93428670..93431519-chr1:93436663..93439033,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1011663	1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10747454	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10874752	0.81[JPT][hapmap]
rs11164838	0.81[JPT][hapmap]
rs11164851	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164854	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12049007	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12120036	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12130044	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12133990	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12144226	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1415069	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1678784	0.82[ASN][1000 genomes]
rs2086314	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2127398	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2127400	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28561471	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3943283	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4515797	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4847226	0.87[ASN][1000 genomes]
rs4847386	0.81[JPT][hapmap]
rs4847389	0.83[ASN][1000 genomes]
rs514235	0.87[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs521428	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs534409	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs567613	0.87[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs594527	0.82[ASN][1000 genomes]
rs606344	0.82[ASN][1000 genomes]
rs619784	0.82[ASN][1000 genomes]
rs641462	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs660870	0.87[CHB][hapmap];0.82[CHD][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs663112	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6671078	0.86[ASN][1000 genomes]
rs6671268	0.87[CHB][hapmap];0.85[CHD][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs6681429	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7517539	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]
rs7524934	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs753391	0.83[ASN][1000 genomes]
rs770883	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs945630	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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
rs11164850	FAM69A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93427800-93433800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:93428000-93431600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr1:93428000-93431800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr1:93428000-93432200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr1:93428000-93434200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:93428200-93431400	Enhancers	Primary B cells from peripheral blood	blood
7	chr1:93428200-93431400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
8	chr1:93428200-93431600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr1:93428200-93432000	Enhancers	Fetal Thymus	thymus
10	chr1:93428200-93432200	Enhancers	Primary T cells fromperipheralblood	blood
11	chr1:93428200-93432200	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr1:93428200-93433600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr1:93428200-93433600	Weak transcription	Hela-S3	cervix
14	chr1:93428200-93438400	Weak transcription	Brain Angular Gyrus	brain
15	chr1:93428400-93431000	Enhancers	Primary B cells from cord blood	blood
16	chr1:93428400-93433600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:93428400-93433600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:93428400-93433600	Weak transcription	Brain Anterior Caudate	brain
19	chr1:93428400-93433600	Weak transcription	Brain Hippocampus Middle	brain
20	chr1:93428400-93433600	Weak transcription	Fetal Heart	heart
21	chr1:93428400-93435000	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr1:93428400-93438200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr1:93428400-93445800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr1:93428600-93431600	Enhancers	Thymus	Thymus
25	chr1:93428600-93436800	Weak transcription	NHEK	skin
26	chr1:93429000-93432200	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr1:93429200-93431200	Weak transcription	K562	blood
28	chr1:93429200-93432200	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr1:93429200-93438200	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr1:93429400-93431200	Bivalent Enhancer	HepG2	liver
31	chr1:93429400-93433600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr1:93429600-93431600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
33	chr1:93430000-93431000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
34	chr1:93430000-93433400	Weak transcription	GM12878-XiMat	blood
35	chr1:93430200-93431200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr1:93430200-93436600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:93430600-93431000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr1:93430600-93432400	Enhancers	Primary T cells from cord blood	blood
39	chr1:93430800-93431200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr1:93430800-93431200	Flanking Active TSS	Dnd41	blood

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