Variant report

Variant	rs16844790
Chromosome Location	chr2:160968628-160968629
allele	A/G
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	IKZF1	chr2:160968486-160969402	GM12878	blood:	n/a	n/a
2	NFIC	chr2:160968614-160969319	GM12878	blood:	n/a	n/a
3	CUX1	chr2:160968604-160969151	GM12878	blood:	n/a	n/a
4	ZNF384	chr2:160968607-160969094	GM12878	blood:	n/a	n/a
5	EBF1	chr2:160968628-160969255	GM12878	blood:	n/a	n/a
6	RELA	chr2:160968515-160969198	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ITGB6	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1037694	0.82[LWK][hapmap]
rs10497212	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12478287	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16844742	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16844802	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17284082	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs28867432	0.80[EUR][1000 genomes]
rs2925754	0.88[GIH][hapmap];0.87[TSI][hapmap]
rs3111395	0.87[CHB][hapmap]
rs3111397	0.87[ASW][hapmap];0.87[CHB][hapmap];0.88[GIH][hapmap];0.87[LWK][hapmap];0.88[MKK][hapmap];0.87[TSI][hapmap]
rs34347603	0.88[ASN][1000 genomes]
rs4076843	0.82[CHB][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4078235	0.88[ASN][1000 genomes]
rs4580348	0.82[MKK][hapmap]
rs4595921	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4664316	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4665146	0.91[CEU][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs4665154	0.83[CHB][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4665156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55759330	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs58716738	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60454853	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60915384	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62175380	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62175383	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs62177892	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72967898	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72969807	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72969809	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72975471	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72975474	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72977408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72978513	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72978520	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72978527	0.83[EUR][1000 genomes]
rs72979930	0.91[ASN][1000 genomes]
rs7557804	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7573469	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7581712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7603686	0.87[CHB][hapmap];0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv459929	chr2:160963603-161079435	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv583497	chr2:160963603-161079435	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv875346	chr2:160965335-161044155	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1001502	chr2:160967864-161079450	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:160953200-160970800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr2:160954600-160970800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr2:160954600-160993000	Weak transcription	Duodenum Mucosa	Duodenum
4	chr2:160955800-160968800	Weak transcription	Fetal Muscle Trunk	muscle
5	chr2:160957000-160970200	Weak transcription	Pancreas	Pancrea
6	chr2:160957400-160981200	Weak transcription	Lung	lung
7	chr2:160959200-161004200	Weak transcription	Gastric	stomach
8	chr2:160959400-160985200	Weak transcription	Esophagus	oesophagus
9	chr2:160959400-161032800	Weak transcription	Psoas Muscle	Psoas
10	chr2:160962400-160970800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:160962800-160971000	Strong transcription	Placenta Amnion	Placenta Amnion
12	chr2:160963800-160969200	Strong transcription	Skeletal Muscle Male	skeletal muscle
13	chr2:160964200-160993600	Weak transcription	Fetal Muscle Leg	muscle
14	chr2:160964400-160993600	Weak transcription	Fetal Intestine Large	intestine
15	chr2:160964800-160970800	Weak transcription	Stomach Mucosa	stomach
16	chr2:160965600-160969200	Genic enhancers	HMEC	breast
17	chr2:160965800-160969600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr2:160966200-160969000	Strong transcription	Fetal Intestine Small	intestine
19	chr2:160966400-160970600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr2:160966400-160980200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr2:160967000-160969400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr2:160967200-160970400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr2:160967200-160979000	Weak transcription	HSMM	muscle
24	chr2:160967400-160968800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr2:160967600-160970400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr2:160967600-160970800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr2:160968000-160970200	Weak transcription	NHEK	skin
28	chr2:160968200-160971000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr2:160968400-160969200	Flanking Active TSS	GM12878-XiMat	blood
30	chr2:160968600-160968800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:160968600-160977400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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