Variant report

Variant	rs655934
Chromosome Location	chr11:86212745-86212746
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:86210913..86213504-chr11:86383764..86386048,2	MCF-7	breast:
2	chr11:86193697..86195389-chr11:86211197..86213851,2	MCF-7	breast:
3	chr11:86209598..86213474-chr11:86222640..86227259,4	K562	blood:
4	chr11:86211974..86214956-chr11:86224089..86226372,2	K562	blood:
5	chr11:86209488..86213127-chr11:86228780..86231761,3	K562	blood:

Extended variants
information (count: 97 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10431169	0.81[CHB][hapmap]
rs10501620	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs10501621	0.82[CHB][hapmap]
rs147045	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs1841066	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[ASN][1000 genomes]
rs2279046	0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap];0.85[ASN][1000 genomes]
rs2446226	0.84[ASN][1000 genomes]
rs2446228	0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap];0.92[ASN][1000 genomes]
rs2446229	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2446231	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2511090	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36043971	0.82[ASN][1000 genomes]
rs3781812	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs498981	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs501362	0.94[ASN][1000 genomes]
rs502749	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs503583	0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs509870	0.82[ASN][1000 genomes]
rs511884	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs525764	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs531908	0.94[ASN][1000 genomes]
rs535652	0.95[CHB][hapmap];0.85[CHD][hapmap];0.83[ASN][1000 genomes]
rs553351	1.00[CHB][hapmap];0.82[CHD][hapmap];0.84[JPT][hapmap];0.81[LWK][hapmap];0.90[ASN][1000 genomes]
rs582976	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs585527	0.87[ASN][1000 genomes]
rs588287	0.95[CHB][hapmap];0.91[CHD][hapmap];0.83[ASN][1000 genomes]
rs589174	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs589368	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs590401	0.91[CHB][hapmap]
rs593853	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs594106	0.81[ASN][1000 genomes]
rs596056	0.95[CHB][hapmap];0.89[ASN][1000 genomes]
rs597296	0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs597793	0.95[ASN][1000 genomes]
rs598187	0.87[ASN][1000 genomes]
rs601300	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs601824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs603890	0.85[ASN][1000 genomes]
rs605251	0.91[CHB][hapmap];0.88[CHD][hapmap]
rs605618	0.95[CHB][hapmap];0.88[CHD][hapmap];0.81[ASN][1000 genomes]
rs606546	0.84[ASN][1000 genomes]
rs608180	0.82[ASN][1000 genomes]
rs609848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs610842	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[ASN][1000 genomes]
rs612163	0.95[CHB][hapmap];0.94[CHD][hapmap];0.85[ASN][1000 genomes]
rs613412	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs616018	0.89[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs618513	0.91[CHB][hapmap];0.91[CHD][hapmap]
rs61904415	0.82[ASN][1000 genomes]
rs619195	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs619472	0.89[ASN][1000 genomes]
rs623478	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs624236	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs624843	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs624870	0.90[CHB][hapmap]
rs625925	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs628406	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs628449	0.94[ASN][1000 genomes]
rs630438	0.92[ASN][1000 genomes]
rs632538	0.85[ASN][1000 genomes]
rs634509	0.95[CHB][hapmap];0.91[CHD][hapmap];0.84[ASN][1000 genomes]
rs635934	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs636485	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs638041	0.95[CHB][hapmap];0.91[CHD][hapmap];0.85[ASN][1000 genomes]
rs640310	0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs642278	0.92[ASN][1000 genomes]
rs643950	0.83[ASN][1000 genomes]
rs644086	0.86[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.81[MEX][hapmap];0.91[ASN][1000 genomes]
rs646691	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs646798	0.85[ASN][1000 genomes]
rs648798	1.00[CHB][hapmap];0.82[CHD][hapmap];0.81[ASN][1000 genomes]
rs651089	0.91[CHB][hapmap];0.88[CHD][hapmap]
rs653779	0.95[CHB][hapmap];0.94[CHD][hapmap];0.85[ASN][1000 genomes]
rs655868	0.81[ASN][1000 genomes]
rs658166	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs659405	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs661083	0.85[ASN][1000 genomes]
rs661972	0.85[ASN][1000 genomes]
rs662361	0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap];0.85[ASN][1000 genomes]
rs663262	0.90[CHB][hapmap]
rs668270	0.85[ASN][1000 genomes]
rs668272	0.89[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.85[YRI][hapmap]
rs670602	0.92[ASN][1000 genomes]
rs674250	0.85[ASN][1000 genomes]
rs677700	0.90[CHB][hapmap]
rs679076	0.91[CHB][hapmap];0.94[CHD][hapmap]
rs679382	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs680846	0.81[ASN][1000 genomes]
rs681158	0.85[ASN][1000 genomes]
rs687804	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs689039	0.84[ASN][1000 genomes]
rs694952	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7130920	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap];0.88[ASN][1000 genomes]
rs9645702	0.84[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs655934	PCF11	cis	parietal	SCAN
rs655934	TMEM126A	cis	cerebellum	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86160200-86221000	Weak transcription	Primary T cells from cord blood	blood
2	chr11:86172400-86227000	Weak transcription	Brain Cingulate Gyrus	brain
3	chr11:86187600-86218600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr11:86189200-86222600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr11:86189600-86221600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr11:86195200-86222200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr11:86196200-86213600	Weak transcription	Brain Germinal Matrix	brain
8	chr11:86198600-86222800	Weak transcription	Esophagus	oesophagus
9	chr11:86202800-86226400	Weak transcription	Fetal Lung	lung
10	chr11:86204000-86222200	Weak transcription	Colon Smooth Muscle	Colon
11	chr11:86204600-86220000	Weak transcription	Colonic Mucosa	Colon
12	chr11:86206800-86214200	Weak transcription	Fetal Muscle Leg	muscle
13	chr11:86206800-86214600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr11:86206800-86214800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr11:86207000-86213400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr11:86209000-86214400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr11:86209000-86214400	Weak transcription	HUVEC	blood vessel
18	chr11:86209200-86213000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr11:86209200-86213200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr11:86209200-86213400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr11:86209200-86213400	Weak transcription	Adipose Nuclei	Adipose
22	chr11:86209200-86213800	Weak transcription	Ovary	ovary
23	chr11:86209200-86213800	Weak transcription	Spleen	Spleen
24	chr11:86209200-86214200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr11:86209200-86214400	Weak transcription	Fetal Muscle Trunk	muscle
26	chr11:86209200-86214600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr11:86209200-86214600	Weak transcription	Osteobl	bone
28	chr11:86209200-86214800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr11:86209200-86215000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr11:86209200-86216600	Weak transcription	Fetal Stomach	stomach
31	chr11:86209200-86218800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr11:86209200-86219600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr11:86209200-86221200	Weak transcription	NH-A	brain
34	chr11:86209200-86223600	Weak transcription	Brain Angular Gyrus	brain
35	chr11:86209200-86226600	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr11:86209400-86213200	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr11:86209400-86213600	Weak transcription	Aorta	Aorta
38	chr11:86209400-86214400	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr11:86209400-86215000	Weak transcription	HSMMtube	muscle
40	chr11:86209400-86219200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr11:86209400-86220000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr11:86209400-86221600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr11:86209400-86221600	Weak transcription	HSMM	muscle
44	chr11:86209600-86218400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr11:86209600-86221800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr11:86209800-86213600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr11:86209800-86218200	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr11:86210000-86212800	Enhancers	Fetal Intestine Large	intestine
49	chr11:86210200-86213000	Enhancers	Fetal Intestine Small	intestine
50	chr11:86210400-86212800	Enhancers	K562	blood

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