Variant report

Variant	rs601646
Chromosome Location	chr11:86173565-86173566
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:86170892..86174262-chr11:86177724..86181309,3	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1056194	0.86[ASW][hapmap];0.84[LWK][hapmap];0.84[MKK][hapmap];0.81[AFR][1000 genomes]
rs10792854	0.85[AFR][1000 genomes]
rs10898483	0.80[CHB][hapmap]
rs10898484	0.85[AFR][1000 genomes]
rs11234691	0.91[JPT][hapmap]
rs1458383	0.85[ASN][1000 genomes]
rs2125362	0.82[LWK][hapmap]
rs2446224	0.95[CHB][hapmap];0.80[ASN][1000 genomes]
rs2446225	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2446230	0.96[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.84[TSI][hapmap];0.85[YRI][hapmap]
rs2511082	0.95[CHB][hapmap];0.95[CHD][hapmap]
rs2511083	0.87[ASN][1000 genomes]
rs3741004	0.81[AFR][1000 genomes]
rs4944575	0.81[LWK][hapmap]
rs4944580	0.86[ASW][hapmap];0.91[LWK][hapmap];0.88[MKK][hapmap];0.85[AFR][1000 genomes]
rs4944581	0.83[AFR][1000 genomes]
rs579719	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs582282	0.90[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]
rs583594	1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs584953	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs587362	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs610476	0.80[ASN][1000 genomes]
rs610790	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap]
rs611730	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap]
rs614995	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs616794	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs621653	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs631082	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs632873	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs638492	0.90[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]
rs641541	0.96[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.85[YRI][hapmap]
rs643414	0.84[ASN][1000 genomes]
rs647561	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs653715	0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs658324	0.90[CHB][hapmap]
rs6592295	0.81[YRI][hapmap];0.83[AFR][1000 genomes]
rs660372	0.96[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.84[TSI][hapmap];0.85[YRI][hapmap]
rs661163	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs661328	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs663208	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs664613	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs669325	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.98[MKK][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs675775	0.95[CHB][hapmap];0.95[CHD][hapmap];0.83[ASN][1000 genomes]
rs676106	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs677301	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs677643	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs679977	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs681333	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs683899	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7941054	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044081	chr11:86133641-86868560	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv541118	chr11:86133641-86868560	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv898056	chr11:86156848-86304402	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs601646	PRSS23	cis	parietal	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86153200-86187000	Weak transcription	Fetal Kidney	kidney
2	chr11:86157000-86179800	Weak transcription	Fetal Intestine Large	intestine
3	chr11:86158600-86187200	Weak transcription	Duodenum Mucosa	Duodenum
4	chr11:86159600-86196800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr11:86160200-86221000	Weak transcription	Primary T cells from cord blood	blood
6	chr11:86168200-86175600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr11:86169400-86174800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr11:86169800-86176200	Enhancers	NHEK	skin
9	chr11:86169800-86178400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr11:86170200-86187200	Weak transcription	Stomach Mucosa	stomach
11	chr11:86170800-86174600	Strong transcription	Fetal Intestine Small	intestine
12	chr11:86171200-86197800	Weak transcription	Esophagus	oesophagus
13	chr11:86171400-86174200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr11:86171600-86175400	Weak transcription	Psoas Muscle	Psoas
15	chr11:86171600-86180400	Weak transcription	Gastric	stomach
16	chr11:86171800-86173800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr11:86171800-86173800	Weak transcription	Aorta	Aorta
18	chr11:86171800-86175600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr11:86171800-86187200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr11:86171800-86188800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr11:86172000-86173600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr11:86172000-86176800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr11:86172000-86180600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr11:86172200-86174000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr11:86172200-86174000	Weak transcription	Lung	lung
26	chr11:86172200-86174200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr11:86172200-86175400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr11:86172200-86176000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr11:86172200-86177400	Weak transcription	NHLF	lung
30	chr11:86172200-86180600	Weak transcription	Osteobl	bone
31	chr11:86172200-86181000	Weak transcription	NHDF-Ad	bronchial
32	chr11:86172200-86184800	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr11:86172200-86208200	Weak transcription	Pancreas	Pancrea
34	chr11:86172400-86173600	Weak transcription	Stomach Smooth Muscle	stomach
35	chr11:86172400-86179000	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr11:86172400-86183400	Weak transcription	Fetal Heart	heart
37	chr11:86172400-86192800	Weak transcription	Brain Anterior Caudate	brain
38	chr11:86172400-86208400	Weak transcription	Brain Angular Gyrus	brain
39	chr11:86172400-86227000	Weak transcription	Brain Cingulate Gyrus	brain
40	chr11:86172600-86173800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr11:86172600-86174200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr11:86172600-86180400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr11:86172600-86180600	Weak transcription	Fetal Lung	lung
44	chr11:86172600-86180800	Weak transcription	Right Ventricle	heart
45	chr11:86172600-86184600	Weak transcription	HSMM	muscle
46	chr11:86172600-86187200	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr11:86172600-86194800	Weak transcription	Brain Hippocampus Middle	brain
48	chr11:86172800-86173600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr11:86172800-86173600	Weak transcription	Adipose Nuclei	Adipose
50	chr11:86172800-86173800	Weak transcription	Fetal Muscle Trunk	muscle

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