Variant report

Variant	rs3825072
Chromosome Location	chr11:64954053-64954054
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:64953126-64954470	K562	blood:	n/a	n/a
2	POLR2A	chr11:64946681-64957644	K562	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:64897351..64905868-chr11:64946257..64954528,24	K562	blood:
2	chr11:64889868..64892172-chr11:64952017..64954494,2	MCF-7	breast:
3	chr11:64877702..64891058-chr11:64944203..64957091,32	K562	blood:
4	chr11:64852718..64854358-chr11:64953563..64956408,2	MCF-7	breast:
5	chr11:64899984..64902140-chr11:64953523..64955030,2	MCF-7	breast:
6	chr11:64780421..64782168-chr11:64953277..64956161,2	MCF-7	breast:
7	chr11:64877522..64908330-chr11:64931619..64960265,171	MCF-7	breast:
8	chr11:64888312..64893387-chr11:64951706..64955535,4	K562	blood:
9	chr11:64953862..64955424-chr11:64955470..64957493,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000254614	TF binding region
CAPN1	TF binding region
ENSG00000014216	Chromatin interaction
ENSG00000149792	Chromatin interaction
ENSG00000273003	Chromatin interaction
ENSG00000149823	Chromatin interaction
ENSG00000162300	Chromatin interaction
ENSG00000213465	Chromatin interaction
ENSG00000162298	Chromatin interaction
ENSG00000149806	Chromatin interaction
ENSG00000255173	Chromatin interaction
ENSG00000149809	Chromatin interaction
ENSG00000254501	Chromatin interaction
ENSG00000174276	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11605576	0.90[JPT][hapmap]
rs12417272	0.81[ASN][1000 genomes]
rs12420069	0.90[JPT][hapmap]
rs12420456	0.90[JPT][hapmap]
rs12422027	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12800339	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17881590	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17886894	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271448	0.95[JPT][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs2277307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34007842	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34281454	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3782093	0.82[ASW][hapmap];0.90[JPT][hapmap]
rs3953797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58858596	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6591178	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7933509	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526181	chr11:64638041-65257329	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1539 gene(s)	inside rSNPs	diseases
2	nsv897713	chr11:64915042-65000719	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs3825072	SLC22A24	cis	cerebellum	SCAN
rs3825072	DAGLA	cis	parietal	SCAN
rs3825072	LOC728975	cis	brain	BrainEAC
rs3825072	YIF1A	cis	cerebellum	SCAN
rs3825072	SCGB2A2	cis	cerebellum	SCAN
rs3825072	NUDT8	cis	parietal	SCAN
rs3825072	HRASLS2	cis	parietal	SCAN
rs3825072	LRRN4CL	cis	parietal	SCAN
rs3825072	SCGB1A1	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64950400-64954200	Weak transcription	Brain Angular Gyrus	brain
2	chr11:64950400-64955400	Weak transcription	Small Intestine	intestine
3	chr11:64950400-64956200	Weak transcription	Brain Substantia Nigra	brain
4	chr11:64950400-64973200	Weak transcription	Fetal Kidney	kidney
5	chr11:64950600-64957200	Weak transcription	Psoas Muscle	Psoas
6	chr11:64950600-64992400	Weak transcription	Right Atrium	heart
7	chr11:64950800-64956000	Weak transcription	HSMM	muscle
8	chr11:64951000-64955600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr11:64951000-64956200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr11:64951000-64956800	Weak transcription	NH-A	brain
11	chr11:64951000-64959000	Strong transcription	Thymus	Thymus
12	chr11:64951000-64959200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr11:64951000-64973600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr11:64951000-64976200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr11:64951200-64954200	Weak transcription	Brain Hippocampus Middle	brain
16	chr11:64951200-64958400	Strong transcription	NHLF	lung
17	chr11:64951200-64958800	Strong transcription	Skeletal Muscle Male	skeletal muscle
18	chr11:64951200-64959800	Strong transcription	Primary T cells from cord blood	blood
19	chr11:64951200-64961800	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr11:64951200-64962800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr11:64951200-64963000	Strong transcription	Liver	Liver
22	chr11:64951200-64963000	Strong transcription	Fetal Stomach	stomach
23	chr11:64951200-64963200	Strong transcription	Fetal Muscle Trunk	muscle
24	chr11:64951200-64963600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr11:64951200-64968400	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr11:64951200-64976200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr11:64951400-64955000	Strong transcription	NHDF-Ad	bronchial
28	chr11:64951400-64957200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr11:64951400-64957200	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr11:64951400-64958800	Strong transcription	Stomach Smooth Muscle	stomach
31	chr11:64951400-64959200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr11:64951400-64960000	Strong transcription	Adipose Nuclei	Adipose
33	chr11:64951400-64963400	Strong transcription	Fetal Muscle Leg	muscle
34	chr11:64951400-64968000	Strong transcription	Primary B cells from peripheral blood	blood
35	chr11:64951400-64979200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr11:64951600-64954200	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr11:64951600-64976400	Weak transcription	Fetal Brain Male	brain
38	chr11:64951600-64979600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr11:64951800-64954400	Strong transcription	Colonic Mucosa	Colon
40	chr11:64951800-64958200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr11:64951800-64958200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr11:64951800-64958400	Strong transcription	Lung	lung
43	chr11:64951800-64958400	Strong transcription	Spleen	Spleen
44	chr11:64951800-64958600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr11:64951800-64958800	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr11:64951800-64959000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr11:64951800-64963200	Strong transcription	Fetal Intestine Large	intestine
48	chr11:64951800-64968800	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr11:64951800-64969000	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr11:64952000-64958600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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