Variant report

Variant	rs11164854
Chromosome Location	chr1:93443043-93443044
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RELA	chr1:93443029-93443734	GM18526	blood:	n/a	n/a
2	SP1	chr1:93442883-93443689	GM12878	blood:	n/a	n/a
3	NFIC	chr1:93442977-93443812	GM12878	blood:	n/a	n/a
4	BHLHE40	chr1:93442759-93443729	GM12878	blood:	n/a	n/a
5	ATF2	chr1:93443001-93443721	GM12878	blood:	n/a	n/a
6	RUNX3	chr1:93442805-93443817	GM12878	blood:	n/a	n/a
7	MEF2A	chr1:93443015-93443529	GM12878	blood:	n/a	n/a
8	NFIC	chr1:93442740-93443849	GM12878	blood:	n/a	n/a
9	ATF2	chr1:93442854-93443739	GM12878	blood:	n/a	n/a
10	RELA	chr1:93442841-93443789	GM12891	blood:	n/a	n/a
11	RELA	chr1:93442926-93443829	GM18505	blood:	n/a	n/a
12	EP300	chr1:93442933-93443718	GM12878	blood:	n/a	n/a
13	RELA	chr1:93442888-93443721	GM15510	blood:	n/a	n/a
14	RELA	chr1:93443040-93443774	GM19099	blood:	n/a	n/a
15	RELA	chr1:93442951-93443762	GM10847	blood:	n/a	n/a
16	RELA	chr1:93442811-93443761	GM19193	blood:	n/a	n/a
17	IKZF1	chr1:93442959-93443676	GM12878	blood:	n/a	n/a
18	RELA	chr1:93442817-93443794	GM12878	blood:	n/a	n/a
19	RELA	chr1:93442822-93443772	GM18951	blood:	n/a	n/a
20	RELA	chr1:93442944-93443787	GM12892	blood:	n/a	n/a
21	EP300	chr1:93443021-93443630	GM12878	blood:	n/a	n/a
22	MTA3	chr1:93442772-93443837	GM12878	blood:	n/a	n/a
23	FOXM1	chr1:93442975-93443796	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
RN7SL692P	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1011663	1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10747454	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10874752	0.81[JPT][hapmap]
rs11164838	0.81[JPT][hapmap]
rs11164850	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]
rs11164851	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[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12049007	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12120036	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12130044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12133990	0.90[ASN][1000 genomes]
rs12144226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1415069	0.83[ASN][1000 genomes]
rs1678784	0.88[ASN][1000 genomes]
rs2086314	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2127398	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2127400	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28561471	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3943283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4515797	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4847226	0.94[ASN][1000 genomes]
rs4847386	0.81[JPT][hapmap]
rs4847389	0.89[ASN][1000 genomes]
rs514235	0.87[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs521428	0.87[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs534409	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs567613	0.87[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs594527	0.88[ASN][1000 genomes]
rs606344	0.88[ASN][1000 genomes]
rs619784	0.88[ASN][1000 genomes]
rs641462	0.85[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs660870	0.87[CHB][hapmap];0.82[CHD][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs663112	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6671078	0.84[ASN][1000 genomes]
rs6671268	0.87[CHB][hapmap];0.85[CHD][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs6681429	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7517539	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]
rs7524934	1.00[ASW][hapmap];1.00[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];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs753391	0.89[ASN][1000 genomes]
rs770883	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs770884	0.84[ASN][1000 genomes]
rs945630	0.83[CEU][hapmap];0.90[EUR][1000 genomes];0.94[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
rs11164854	FAM69A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93428400-93445800	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr1:93433200-93445000	Enhancers	Primary B cells from cord blood	blood
3	chr1:93434200-93445600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr1:93438000-93443600	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr1:93438200-93443400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
6	chr1:93438800-93446000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:93439000-93444400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr1:93439400-93446400	Weak transcription	Thymus	Thymus
9	chr1:93439600-93445600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr1:93439600-93446000	Weak transcription	Fetal Thymus	thymus
11	chr1:93439600-93446400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr1:93441000-93447800	Enhancers	Primary B cells from peripheral blood	blood
13	chr1:93441400-93443600	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr1:93441600-93445400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr1:93441600-93445600	Weak transcription	Primary T cells from cord blood	blood
16	chr1:93441600-93445600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:93441600-93446000	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr1:93441600-93446200	Weak transcription	Dnd41	blood
19	chr1:93441800-93443400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr1:93441800-93445800	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr1:93442200-93445800	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr1:93442800-93443600	Flanking Active TSS	GM12878-XiMat	blood
23	chr1:93442800-93448400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr1:93443000-93443200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr1:93443000-93443400	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr1:93443000-93443400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

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