Variant report

Variant	rs7569555
Chromosome Location	chr2:160987608-160987609
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:160981983..160984926-chr2:160986223..160988366,2	K562	blood:

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10454740	0.80[CEU][hapmap]
rs10497208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10929970	0.95[CEU][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10929971	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11885142	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11887337	0.80[CEU][hapmap]
rs11890075	0.80[YRI][hapmap]
rs11895959	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11896610	0.84[YRI][hapmap]
rs11897691	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11902965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12476618	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13027372	0.96[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13394776	0.80[CEU][hapmap]
rs13427061	0.81[CEU][hapmap]
rs1457233	0.80[CEU][hapmap]
rs1457235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1457236	0.88[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1457237	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1457238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1457240	0.81[CEU][hapmap]
rs1471120	0.81[CEU][hapmap]
rs1471121	0.81[CEU][hapmap]
rs16844824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1902622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061288	0.80[CEU][hapmap]
rs2061290	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2168672	0.84[YRI][hapmap]
rs2357773	0.84[CEU][hapmap]
rs2357861	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2715929	0.80[CEU][hapmap]
rs2884268	0.81[ASN][1000 genomes]
rs2925763	0.81[CEU][hapmap]
rs34064895	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34762905	0.85[EUR][1000 genomes]
rs34955537	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35271738	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35720878	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35859214	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3796103	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4233679	0.81[CEU][hapmap]
rs4265965	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4324285	0.81[CEU][hapmap]
rs4426486	0.84[EUR][1000 genomes]
rs4580348	0.85[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4664313	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4664315	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4665160	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6432593	0.81[CEU][hapmap]
rs6432594	0.80[YRI][hapmap]
rs6432600	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6432601	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6432602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6432603	0.84[CEU][hapmap]
rs6729540	0.80[CEU][hapmap]
rs6730023	0.84[LWK][hapmap];0.96[YRI][hapmap]
rs7422400	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs748427	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs7558296	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7558852	0.81[CEU][hapmap]
rs7563574	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7568816	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7579481	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7583743	0.84[CEU][hapmap]
rs7584446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7608267	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs897832	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs996112	0.84[CEU][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7569555	CYTIP	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:160954600-160993000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr2:160959200-161004200	Weak transcription	Gastric	stomach
3	chr2:160959400-161032800	Weak transcription	Psoas Muscle	Psoas
4	chr2:160964200-160993600	Weak transcription	Fetal Muscle Leg	muscle
5	chr2:160964400-160993600	Weak transcription	Fetal Intestine Large	intestine
6	chr2:160971000-160993800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr2:160977400-160988600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:160977600-160988800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr2:160977600-160989200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:160977600-160989600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:160977600-160989600	Strong transcription	HMEC	breast
12	chr2:160980600-160996400	Weak transcription	HSMMtube	muscle
13	chr2:160982800-160993600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr2:160983000-160988000	Weak transcription	Dnd41	blood
15	chr2:160983000-160993800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr2:160983000-160993800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr2:160983200-161005200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr2:160983400-160993600	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr2:160983400-160993600	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr2:160983600-160993800	Weak transcription	Pancreas	Pancrea
21	chr2:160983600-160994000	Weak transcription	Fetal Stomach	stomach
22	chr2:160985200-160993800	Weak transcription	Fetal Intestine Small	intestine
23	chr2:160985400-160993800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr2:160986000-160989400	Weak transcription	NHEK	skin
25	chr2:160987600-160988800	Strong transcription	HSMM	muscle

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