Variant report

Variant	rs6750599
Chromosome Location	chr2:111893869-111893870
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:111893690..111895905-chr2:111918348..111921261,2	MCF-7	breast:
2	chr2:111891793..111893976-chr2:111895224..111897547,2	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs13396983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17558117	0.84[CEU][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs1877331	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1980045	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2015454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2241843	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2241845	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];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36018702	0.92[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3827536	0.96[CEU][hapmap];0.82[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4848393	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4849417	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4849442	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs616084	0.89[ASN][1000 genomes]
rs616130	0.96[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs616582	0.85[CEU][hapmap];0.82[ASN][1000 genomes]
rs6542334	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6746608	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6753785	0.92[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6758181	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs676119	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7567444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9308731	1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[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	nsv874838	chr2:111376870-112046226	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv834331	chr2:111812139-112004678	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6750599	BCL2L11	cis	cerebellum	SCAN
rs6750599	BCL2L11	cis	multi-tissue	Pritchard

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:111881200-111894800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr2:111881200-111904200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:111881200-111909600	Weak transcription	NHLF	lung
4	chr2:111881200-111912800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:111881600-111897200	Weak transcription	Stomach Mucosa	stomach
6	chr2:111881600-111897400	Weak transcription	Stomach Smooth Muscle	stomach
7	chr2:111881600-111901000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr2:111881600-111904200	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr2:111881800-111894400	Weak transcription	Brain Hippocampus Middle	brain
10	chr2:111881800-111900800	Weak transcription	Fetal Brain Male	brain
11	chr2:111881800-111908600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr2:111881800-111909600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr2:111881800-111919800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr2:111883200-111894800	Weak transcription	NHEK	skin
15	chr2:111883400-111907800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr2:111883400-111909400	Weak transcription	Aorta	Aorta
17	chr2:111883400-111912600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr2:111883600-111896200	Weak transcription	Gastric	stomach
19	chr2:111883600-111909400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr2:111883600-111909600	Weak transcription	Small Intestine	intestine
21	chr2:111883800-111897000	Weak transcription	HMEC	breast
22	chr2:111883800-111897600	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr2:111883800-111898400	Weak transcription	Brain Angular Gyrus	brain
24	chr2:111883800-111904000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr2:111884000-111894800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr2:111884000-111901600	Weak transcription	Hela-S3	cervix
27	chr2:111884600-111909400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr2:111884800-111925400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr2:111885800-111895200	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr2:111886000-111896000	Weak transcription	HSMMtube	muscle
31	chr2:111886200-111900800	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr2:111886400-111896600	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr2:111886800-111896800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr2:111887000-111902600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr2:111887400-111896200	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr2:111887400-111912000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr2:111887600-111899400	Weak transcription	Colonic Mucosa	Colon
38	chr2:111887800-111898400	Weak transcription	Fetal Kidney	kidney
39	chr2:111888200-111897200	Weak transcription	A549	lung
40	chr2:111889800-111896200	Weak transcription	Fetal Muscle Leg	muscle
41	chr2:111889800-111900800	Weak transcription	Duodenum Mucosa	Duodenum
42	chr2:111890600-111914400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr2:111891400-111896600	Weak transcription	GM12878-XiMat	blood
44	chr2:111891400-111897200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr2:111891400-111905800	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr2:111891800-111894600	Strong transcription	Primary B cells from peripheral blood	blood
47	chr2:111891800-111902600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr2:111892400-111896600	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr2:111892400-111899000	Strong transcription	Fetal Intestine Large	intestine
50	chr2:111892600-111895200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast

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