Variant report

Variant	rs9308731
Chromosome Location	chr2:111908262-111908263
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:111904094..111906094-chr2:111907490..111909411,2	K562	blood:
2	chr2:111877254..111880107-chr2:111907891..111910669,3	MCF-7	breast:
3	chr2:111877202..111881841-chr2:111904437..111911865,11	K562	blood:

Variant related genes	Relation type
ENSG00000153094	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10189015	0.83[CHB][hapmap]
rs13396983	1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17558117	0.87[ASW][hapmap];0.84[CEU][hapmap];0.82[CHB][hapmap];0.85[GIH][hapmap]
rs1877331	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1980045	0.96[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2015454	0.87[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2241843	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2241845	1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36018702	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3789061	0.83[CHB][hapmap]
rs3789065	0.83[CHB][hapmap]
rs3789068	0.83[CHB][hapmap]
rs3827536	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4848393	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4849417	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4849442	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs616084	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs616130	0.96[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs616582	0.85[CEU][hapmap];0.82[CHB][hapmap]
rs6542334	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6746608	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6750599	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]
rs6753785	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6758181	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs676119	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7567444	0.87[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
3	esv1803356	chr2:111899783-112662597	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv428402	chr2:111899783-112662597	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	esv1801950	chr2:111899783-112746937	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	esv2757825	chr2:111899783-112746937	Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
7	esv2759083	chr2:111899783-112746937	Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9308731	BCL2L11	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:111881200-111909600	Weak transcription	NHLF	lung
2	chr2:111881200-111912800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr2:111881800-111908600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr2:111881800-111909600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr2:111881800-111919800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr2:111883400-111909400	Weak transcription	Aorta	Aorta
7	chr2:111883400-111912600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr2:111883600-111909400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr2:111883600-111909600	Weak transcription	Small Intestine	intestine
10	chr2:111884600-111909400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr2:111884800-111925400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr2:111887400-111912000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:111890600-111914400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr2:111893600-111909200	Weak transcription	Brain Substantia Nigra	brain
15	chr2:111893600-111913400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:111893600-111916800	Weak transcription	HSMM	muscle
17	chr2:111893600-111918600	Weak transcription	Colon Smooth Muscle	Colon
18	chr2:111893800-111908400	Weak transcription	Spleen	Spleen
19	chr2:111894200-111917200	Weak transcription	NH-A	brain
20	chr2:111894400-111909600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr2:111895000-111912800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr2:111895400-111909600	Weak transcription	Brain Hippocampus Middle	brain
23	chr2:111896600-111908800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr2:111897600-111912800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr2:111897600-111913000	Weak transcription	Stomach Mucosa	stomach
26	chr2:111897800-111909000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:111897800-111909000	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr2:111897800-111909200	Weak transcription	Esophagus	oesophagus
29	chr2:111897800-111909600	Weak transcription	Pancreas	Pancrea
30	chr2:111897800-111910000	Weak transcription	Stomach Smooth Muscle	stomach
31	chr2:111897800-111910600	Strong transcription	HepG2	liver
32	chr2:111897800-111912400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr2:111897800-111912600	Weak transcription	Brain Anterior Caudate	brain
34	chr2:111897800-111916600	Weak transcription	Psoas Muscle	Psoas
35	chr2:111898000-111911400	Strong transcription	Liver	Liver
36	chr2:111898200-111909400	Weak transcription	Fetal Muscle Leg	muscle
37	chr2:111898200-111912600	Weak transcription	NHEK	skin
38	chr2:111898800-111909200	Weak transcription	Brain Angular Gyrus	brain
39	chr2:111898800-111909400	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr2:111898800-111909600	Weak transcription	Lung	lung
41	chr2:111898800-111912400	Weak transcription	HMEC	breast
42	chr2:111898800-111912800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:111898800-111920600	Weak transcription	Fetal Kidney	kidney
44	chr2:111899800-111909200	Weak transcription	Colonic Mucosa	Colon
45	chr2:111899800-111909600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr2:111902400-111909400	Weak transcription	HSMMtube	muscle
47	chr2:111902800-111912400	Weak transcription	Hela-S3	cervix
48	chr2:111902800-111915200	Weak transcription	Fetal Brain Female	brain
49	chr2:111904400-111920800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr2:111904800-111912800	Strong transcription	Fetal Thymus	thymus

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