Variant report

Variant	rs6716753
Chromosome Location	chr2:231097129-231097130
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10198539	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10201872	0.84[CEU][hapmap];0.87[GIH][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10202244	0.84[CEU][hapmap];0.87[GIH][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10209615	0.84[GIH][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10498246	0.94[CEU][hapmap];0.94[EUR][1000 genomes]
rs12694867	1.00[CHD][hapmap]
rs13384787	0.84[CEU][hapmap];0.84[GIH][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13385151	0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13397985	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13426106	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1946410	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28445040	0.94[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28693552	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34855578	0.94[EUR][1000 genomes]
rs35857956	0.94[EUR][1000 genomes]
rs6436922	1.00[CEU][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6705808	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6710287	1.00[CHD][hapmap]
rs6710297	1.00[CHD][hapmap];0.83[GIH][hapmap]
rs6743984	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7423615	0.94[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7557418	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7563433	0.94[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7584894	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs890581	0.84[CEU][hapmap]
rs9989735	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9989746	0.84[CEU][hapmap];0.81[GIH][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9989835	0.94[CEU][hapmap];0.94[EUR][1000 genomes]
rs9989899	0.94[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001562	chr2:230862717-231187043	Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv536156	chr2:230862717-231187043	Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv498047	chr2:230951712-231250489	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv869834	chr2:231045013-231139827	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv998291	chr2:231045388-231136278	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv584666	chr2:231050715-231106621	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv18000	chr2:231072978-231467847	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Crohn's disease	23128233	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6716753	TRIP12	cis	parietal	SCAN
rs6716753	SP110	Cis_1M	lymphoblastoid	RTeQTL
rs6716753	SP140	cis	lymphoblastoid	seeQTL
rs6716753	SP140	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231090200-231170000	Weak transcription	Spleen	Spleen
2	chr2:231091000-231102600	Weak transcription	Small Intestine	intestine
3	chr2:231092600-231118400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr2:231093200-231113000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr2:231096000-231101600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr2:231096000-231102600	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr2:231096200-231097800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr2:231096200-231101600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr2:231096400-231097200	Enhancers	Primary T cells fromperipheralblood	blood
10	chr2:231096400-231097600	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr2:231096400-231100200	Genic enhancers	Primary B cells from peripheral blood	blood
12	chr2:231096600-231097200	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr2:231096600-231097800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr2:231096800-231097200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
15	chr2:231096800-231097400	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr2:231096800-231098800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr2:231097000-231097200	Enhancers	Primary B cells from cord blood	blood
18	chr2:231097000-231097200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr2:231097000-231097200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr2:231097000-231097200	Enhancers	NH-A	brain
21	chr2:231097000-231097600	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr2:231097000-231097800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr2:231097000-231098800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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