Variant report

Variant	rs11895959
Chromosome Location	chr2:160968838-160968839
allele	G/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	IRF4	chr2:160968668-160969216	GM12878	blood:	n/a	chr2:160969107-160969121
2	PBX3	chr2:160968834-160969006	GM12878	blood:	n/a	n/a
3	ATF2	chr2:160968650-160969144	GM12878	blood:	n/a	n/a
4	RUNX3	chr2:160968658-160969320	GM12878	blood:	n/a	n/a
5	BCL11A	chr2:160968807-160969070	GM12878	blood:	n/a	n/a
6	RUNX3	chr2:160968690-160969299	GM12878	blood:	n/a	n/a
7	PAX5	chr2:160968786-160969132	GM12878	blood:	n/a	n/a
8	EBF1	chr2:160968793-160969117	GM12878	blood:	n/a	n/a
9	IKZF1	chr2:160968486-160969402	GM12878	blood:	n/a	n/a
10	PAX5	chr2:160968756-160969087	GM12878	blood:	n/a	n/a
11	NFIC	chr2:160968614-160969319	GM12878	blood:	n/a	n/a
12	CUX1	chr2:160968604-160969151	GM12878	blood:	n/a	n/a
13	ZNF384	chr2:160968607-160969094	GM12878	blood:	n/a	n/a
14	EBF1	chr2:160968628-160969255	GM12878	blood:	n/a	n/a
15	EP300	chr2:160968655-160969088	GM12878	blood:	n/a	n/a
16	BATF	chr2:160968686-160969071	GM12878	blood:	n/a	n/a
17	BCL11A	chr2:160968700-160969078	GM12878	blood:	n/a	n/a
18	EP300	chr2:160968657-160969274	GM12878	blood:	n/a	n/a
19	EBF1	chr2:160968802-160969080	GM12878	blood:	n/a	n/a
20	PAX5	chr2:160968742-160969252	GM12878	blood:	n/a	n/a
21	BHLHE40	chr2:160968635-160969253	GM12878	blood:	n/a	n/a
22	RELA	chr2:160968515-160969198	GM12878	blood:	n/a	n/a
23	CHD2	chr2:160968788-160969047	GM12878	blood:	n/a	n/a
24	POU2F2	chr2:160968708-160969242	GM12878	blood:	n/a	chr2:160968788-160968806 chr2:160968791-160968802 chr2:160968790-160968805 chr2:160968791-160968802 chr2:160968793-160968803 chr2:160968790-160968804 chr2:160969029-160969042 chr2:160968786-160968808 chr2:160968791-160968804 chr2:160968793-160968803 chr2:160968787-160968800 chr2:160968792-160968802
25	BATF	chr2:160968776-160969110	GM12878	blood:	n/a	n/a
26	EP300	chr2:160968765-160968997	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:160968652..160971180-chr2:161059515..161062161,2	MCF-7	breast:

Variant related genes	Relation type
ITGB6	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10497208	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10929970	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10929971	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11885142	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11897691	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11902965	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13027372	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1457235	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1457236	0.80[AMR][1000 genomes]
rs1457237	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1457238	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16844824	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1902622	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2061290	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2357861	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34064895	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34955537	0.82[ASN][1000 genomes]
rs35271738	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35720878	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35859214	0.81[ASN][1000 genomes]
rs3796103	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4265965	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4426486	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4580348	0.92[ASN][1000 genomes]
rs4664313	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4664314	0.86[ASN][1000 genomes]
rs4664315	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4665160	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6432600	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6432601	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6432602	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6735425	0.80[AFR][1000 genomes]
rs6758074	0.86[AFR][1000 genomes]
rs7422400	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7558296	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7563574	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7568816	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7569555	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7579481	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7584446	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7599127	0.83[AFR][1000 genomes]
rs7608267	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs897832	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]

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:30 , 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	chr2:160957000-160970200	Weak transcription	Pancreas	Pancrea
5	chr2:160957400-160981200	Weak transcription	Lung	lung
6	chr2:160959200-161004200	Weak transcription	Gastric	stomach
7	chr2:160959400-160985200	Weak transcription	Esophagus	oesophagus
8	chr2:160959400-161032800	Weak transcription	Psoas Muscle	Psoas
9	chr2:160962400-160970800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:160962800-160971000	Strong transcription	Placenta Amnion	Placenta Amnion
11	chr2:160963800-160969200	Strong transcription	Skeletal Muscle Male	skeletal muscle
12	chr2:160964200-160993600	Weak transcription	Fetal Muscle Leg	muscle
13	chr2:160964400-160993600	Weak transcription	Fetal Intestine Large	intestine
14	chr2:160964800-160970800	Weak transcription	Stomach Mucosa	stomach
15	chr2:160965600-160969200	Genic enhancers	HMEC	breast
16	chr2:160965800-160969600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr2:160966200-160969000	Strong transcription	Fetal Intestine Small	intestine
18	chr2:160966400-160970600	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr2:160966400-160980200	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr2:160967000-160969400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr2:160967200-160970400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:160967200-160979000	Weak transcription	HSMM	muscle
23	chr2:160967600-160970400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr2:160967600-160970800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr2:160968000-160970200	Weak transcription	NHEK	skin
26	chr2:160968200-160971000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:160968400-160969200	Flanking Active TSS	GM12878-XiMat	blood
28	chr2:160968600-160977400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr2:160968800-160969000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:160968800-160970200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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