Variant report

Variant	rs6671268
Chromosome Location	chr1:93439821-93439822
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	ZC3H11A	chr1:93439661-93439933	K562	blood:	n/a	n/a

Variant related genes	Relation type
RNU6-970P	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1011663	0.87[CHB][hapmap];0.81[CHD][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs10747454	0.88[ASN][1000 genomes]
rs10874752	0.88[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11164827	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs11164838	0.88[CHB][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap]
rs11164848	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11164849	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11164850	0.87[CHB][hapmap];0.85[CHD][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs11164851	0.87[CHB][hapmap];0.85[CHD][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs11164854	0.87[CHB][hapmap];0.85[CHD][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs12049007	0.81[ASN][1000 genomes]
rs12092304	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12120036	0.81[ASN][1000 genomes]
rs12130044	0.87[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs12133990	0.85[ASN][1000 genomes]
rs12144226	0.85[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs12747275	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1678784	0.86[ASN][1000 genomes]
rs2086314	0.81[ASN][1000 genomes]
rs2127398	0.81[ASN][1000 genomes]
rs2127400	0.81[ASN][1000 genomes]
rs28561471	0.88[ASN][1000 genomes]
rs3943283	0.87[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs4515797	0.90[ASN][1000 genomes]
rs4847226	0.80[ASN][1000 genomes]
rs4847386	0.94[ASW][hapmap];0.84[CEU][hapmap];0.87[CHB][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4847389	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs514235	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs521428	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs534409	0.90[ASN][1000 genomes]
rs567613	0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs594527	0.88[ASN][1000 genomes]
rs606344	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs619784	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs641462	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]
rs655026	0.81[CEU][hapmap]
rs660870	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs663112	0.83[ASN][1000 genomes]
rs6671078	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6681240	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6681345	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6681429	0.81[ASN][1000 genomes]
rs7517539	0.81[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs7524934	0.87[CHB][hapmap];0.81[CHD][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs753391	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs770883	0.87[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs770884	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs945630	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6671268	CDC73	trans	cerebellum	SCAN
rs6671268	FAM69A	cis	Artery Tibial	GTEx
rs6671268	MTF2	cis	Skin Sun Exposed Lower leg	GTEx
rs6671268	BARHL2	cis	parietal	SCAN

Chromatin state (count:32 , 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	chr1:93435400-93440600	Enhancers	Primary B cells from peripheral blood	blood
5	chr1:93436200-93441800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:93436600-93440600	Weak transcription	Pancreas	Pancrea
7	chr1:93437000-93441800	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr1:93437600-93441400	Enhancers	Primary T cells fromperipheralblood	blood
9	chr1:93438000-93441800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr1:93438000-93443600	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr1:93438200-93443400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr1:93438600-93440000	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr1:93438800-93440600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr1:93438800-93446000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:93439000-93444400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:93439200-93440400	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr1:93439400-93440400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr1:93439400-93440600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr1:93439400-93441600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:93439400-93446400	Weak transcription	Thymus	Thymus
21	chr1:93439600-93440400	Enhancers	GM12878-XiMat	blood
22	chr1:93439600-93440600	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr1:93439600-93440600	Weak transcription	Dnd41	blood
24	chr1:93439600-93441200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr1:93439600-93441200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr1:93439600-93441200	Weak transcription	K562	blood
27	chr1:93439600-93443000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr1:93439600-93445600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr1:93439600-93446000	Weak transcription	Fetal Thymus	thymus
30	chr1:93439600-93446400	Weak transcription	Duodenum Mucosa	Duodenum
31	chr1:93439800-93440200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr1:93439800-93441200	Weak transcription	Primary T cells from cord blood	blood

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