Variant report

Variant	rs7524934
Chromosome Location	chr1:93444735-93444736
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	NFIC	chr1:93444284-93445051	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:93331313..93333076-chr1:93443044..93445998,2	K562	blood:

Variant related genes	Relation type
RN7SL692P	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1011663	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10747454	0.81[EUR][1000 genomes];0.90[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];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]
rs11164851	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];0.84[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11164854	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]
rs12049007	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12120036	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12130044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12133990	0.87[ASN][1000 genomes]
rs12144226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1415069	0.80[ASN][1000 genomes]
rs1678784	0.91[ASN][1000 genomes]
rs2086314	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2127398	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2127400	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28561471	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3943283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4515797	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4847226	0.97[ASN][1000 genomes]
rs4847386	0.81[JPT][hapmap]
rs4847389	0.86[ASN][1000 genomes]
rs514235	0.87[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs521428	0.87[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs534409	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs567613	0.87[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs594527	0.91[ASN][1000 genomes]
rs606344	0.91[ASN][1000 genomes]
rs619784	0.91[ASN][1000 genomes]
rs641462	0.85[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs660870	0.87[CHB][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs663112	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6671078	0.81[ASN][1000 genomes]
rs6671268	0.87[CHB][hapmap];0.81[CHD][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs6681429	0.83[ASN][1000 genomes]
rs7517539	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	0.90[ASN][1000 genomes]
rs770883	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs770884	0.81[ASN][1000 genomes]
rs945630	0.83[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[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
rs7524934	FAM69A	cis	Thyroid	GTEx
rs7524934	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	chr1:93438800-93446000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:93439400-93446400	Weak transcription	Thymus	Thymus
6	chr1:93439600-93445600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr1:93439600-93446000	Weak transcription	Fetal Thymus	thymus
8	chr1:93439600-93446400	Weak transcription	Duodenum Mucosa	Duodenum
9	chr1:93441000-93447800	Enhancers	Primary B cells from peripheral blood	blood
10	chr1:93441600-93445400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr1:93441600-93445600	Weak transcription	Primary T cells from cord blood	blood
12	chr1:93441600-93445600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:93441600-93446000	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr1:93441600-93446200	Weak transcription	Dnd41	blood
15	chr1:93441800-93445800	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr1:93442200-93445800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr1:93442800-93448400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr1:93443400-93445600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr1:93443400-93446000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr1:93443600-93445400	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr1:93444000-93444800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr1:93444200-93446200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr1:93444200-93448800	Enhancers	Primary T cells fromperipheralblood	blood
24	chr1:93444400-93445400	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr1:93444600-93444800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr1:93444600-93445400	Active TSS	GM12878-XiMat	blood

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