Variant report

Variant	rs677909
Chromosome Location	chr11:85757589-85757590
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:85755861..85758384-chr11:85778861..85780812,2	MCF-7	breast:
2	chr11:85756990..85760040-chr11:85954686..85957890,3	K562	blood:
3	chr11:85755134..85758081-chr11:85773891..85777241,3	K562	blood:
4	chr11:85755599..85757870-chr11:85777185..85779857,2	K562	blood:

Variant related genes	Relation type
ENSG00000073921	Chromatin interaction
ENSG00000074266	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10751134	0.87[ASW][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap]
rs10792830	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs10792831	0.86[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs10792832	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs10898438	0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs10898439	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs1214669	0.90[ASN][1000 genomes]
rs1898895	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1949221	0.93[ASN][1000 genomes]
rs1973630	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1996108	0.80[AFR][1000 genomes]
rs2458493	1.00[YRI][hapmap]
rs2458496	1.00[YRI][hapmap]
rs2458500	1.00[YRI][hapmap]
rs2508379	0.81[AMR][1000 genomes]
rs2508381	0.93[ASN][1000 genomes]
rs2508690	0.84[ASN][1000 genomes]
rs2508691	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2508692	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2508693	0.95[ASN][1000 genomes]
rs2508696	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2508697	0.90[ASN][1000 genomes]
rs2509608	1.00[YRI][hapmap]
rs3016240	0.99[ASN][1000 genomes]
rs3016786	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3851178	0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs3851179	0.87[ASW][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs475639	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs478711	0.88[ASN][1000 genomes]
rs480781	0.85[EUR][1000 genomes]
rs484154	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs489486	1.00[YRI][hapmap]
rs493254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4944560	0.90[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs497711	0.84[AFR][1000 genomes]
rs497816	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs501505	0.81[ASN][1000 genomes]
rs519778	0.98[ASN][1000 genomes]
rs526904	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs527162	1.00[ASW][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap]
rs529904	0.89[ASN][1000 genomes]
rs532470	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs535590	0.88[EUR][1000 genomes]
rs536841	0.86[ASW][hapmap];0.96[CEU][hapmap];0.83[GIH][hapmap];0.81[LWK][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs541458	0.96[CEU][hapmap];0.91[GIH][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs541674	0.93[ASN][1000 genomes]
rs542126	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs545592	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs553141	0.92[ASN][1000 genomes]
rs561646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs561655	0.80[CEU][hapmap];0.87[GIH][hapmap]
rs563773	0.86[ASN][1000 genomes]
rs565031	0.85[ASN][1000 genomes]
rs565719	0.90[EUR][1000 genomes]
rs572979	0.85[ASN][1000 genomes]
rs587038	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs592297	1.00[ASW][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap]
rs600743	1.00[YRI][hapmap]
rs602222	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs606505	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs609903	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs613222	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs629343	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs631639	0.90[EUR][1000 genomes]
rs636355	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs636772	0.89[ASN][1000 genomes]
rs637304	1.00[YRI][hapmap]
rs639012	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs642949	0.90[ASN][1000 genomes]
rs645299	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs647422	0.98[ASN][1000 genomes]
rs659023	0.91[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap]
rs659863	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs666682	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs669813	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs671686	0.83[ASN][1000 genomes]
rs673751	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs676733	0.87[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs677869	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs682928	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs683494	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs694011	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7114331	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs7114401	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7129687	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs7941541	1.00[ASW][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs7951988	1.00[YRI][hapmap]
rs867611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9804630	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035489	chr11:85502953-85778229	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1053808	chr11:85588919-85757693	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv468769	chr11:85683554-85757589	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv555641	chr11:85683554-85757589	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv898054	chr11:85683554-85772636	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv468771	chr11:85688209-85757589	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv468773	chr11:85688209-85757589	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv555643	chr11:85688209-85757589	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv468774	chr11:85688209-85775059	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv555644	chr11:85688209-85775059	Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	esv1829985	chr11:85740319-85789350	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
12	nsv1050948	chr11:85756325-85968665	Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
13	nsv541117	chr11:85756325-85968665	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs677909	PICALM	cis	cerebellum	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85742800-85758400	Weak transcription	Fetal Intestine Large	intestine
2	chr11:85746600-85762800	Weak transcription	Stomach Mucosa	stomach
3	chr11:85750200-85758200	Weak transcription	Fetal Intestine Small	intestine
4	chr11:85750600-85758800	Weak transcription	Fetal Muscle Trunk	muscle
5	chr11:85751400-85761800	Enhancers	Liver	Liver
6	chr11:85751600-85757600	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr11:85751600-85758200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
8	chr11:85751800-85760600	Enhancers	Primary T cells from cord blood	blood
9	chr11:85751800-85761200	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr11:85752400-85758000	Enhancers	Hela-S3	cervix
11	chr11:85752400-85759000	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr11:85752400-85760600	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr11:85752400-85768400	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr11:85752800-85758400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr11:85752800-85768200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr11:85752800-85776400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr11:85753000-85763000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr11:85753200-85758600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr11:85753200-85759000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr11:85753200-85762200	Enhancers	Adipose Nuclei	Adipose
21	chr11:85753200-85764600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr11:85753200-85768000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr11:85753400-85758000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr11:85753800-85759400	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr11:85754000-85764000	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr11:85754200-85757800	Weak transcription	Primary hematopoietic stem cells	blood
27	chr11:85754200-85764000	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr11:85754200-85765200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr11:85754400-85758400	Weak transcription	Fetal Kidney	kidney
30	chr11:85754400-85759800	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr11:85754400-85763000	Weak transcription	HUVEC	blood vessel
32	chr11:85754400-85768200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr11:85754600-85762600	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr11:85755200-85758200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr11:85755200-85758400	Enhancers	Brain Angular Gyrus	brain
36	chr11:85755200-85761200	Enhancers	Primary T cells fromperipheralblood	blood
37	chr11:85755200-85762800	Weak transcription	Fetal Lung	lung
38	chr11:85755400-85758800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr11:85755600-85761400	Weak transcription	Duodenum Mucosa	Duodenum
40	chr11:85755800-85757600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr11:85755800-85757800	Weak transcription	Stomach Smooth Muscle	stomach
42	chr11:85755800-85758200	Weak transcription	Fetal Thymus	thymus
43	chr11:85755800-85758200	Weak transcription	A549	lung
44	chr11:85755800-85759200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr11:85755800-85759400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr11:85755800-85760600	Enhancers	Brain Substantia Nigra	brain
47	chr11:85755800-85763000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr11:85755800-85764000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr11:85755800-85764000	Weak transcription	HepG2	liver
50	chr11:85756000-85757600	Weak transcription	Right Atrium	heart

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