Variant report

Variant	rs72996302
Chromosome Location	chr2:231259323-231259324
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11675127	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11675135	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11676089	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11677646	0.86[AMR][1000 genomes]
rs11681234	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11681358	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11688362	0.85[AMR][1000 genomes]
rs11692527	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11692602	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17273079	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17332171	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3769849	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55893188	0.89[AMR][1000 genomes]
rs55964110	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56044062	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56052963	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56105857	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56108366	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56251216	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56303947	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6436933	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6706167	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6713447	0.89[AMR][1000 genomes]
rs6713465	0.89[AMR][1000 genomes]
rs6732684	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs6732940	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6748339	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6748445	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6753500	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6761255	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72495174	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72495175	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72495176	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72495180	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72495181	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72495182	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs725202	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72996270	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs72996292	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72996299	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72998203	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7559665	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7563909	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7585646	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7585731	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7589948	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7597033	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv18000	chr2:231072978-231467847	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv3348338	chr2:231160124-231259498	Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv875945	chr2:231172642-231267925	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv869708	chr2:231173700-231267616	Genic enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv3486129	chr2:231175581-231265831	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv3486131	chr2:231175581-231265831	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv2751844	chr2:231179495-231280495	Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1006206	chr2:231179884-231268938	Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv875946	chr2:231184106-231277567	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv875947	chr2:231190446-231281286	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs72996302	SP140L	cis	Whole Blood	GTEx
rs72996302	SP140L	cis	lung	GTEx
rs72996302	SP140L	cis	Adipose Subcutaneous	GTEx
rs72996302	SP140L	cis	Nerve Tibial	GTEx

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231212800-231262400	Weak transcription	K562	blood
2	chr2:231220000-231275800	Weak transcription	Stomach Mucosa	stomach
3	chr2:231222200-231273200	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr2:231223600-231263600	Weak transcription	Fetal Kidney	kidney
5	chr2:231225200-231268000	Weak transcription	Colon Smooth Muscle	Colon
6	chr2:231228800-231260000	Strong transcription	Primary B cells from peripheral blood	blood
7	chr2:231228800-231275600	Weak transcription	Psoas Muscle	Psoas
8	chr2:231232200-231260400	Weak transcription	Fetal Lung	lung
9	chr2:231234200-231274400	Weak transcription	Brain Hippocampus Middle	brain
10	chr2:231234400-231259400	Weak transcription	Fetal Intestine Small	intestine
11	chr2:231236800-231260000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:231237000-231264800	Weak transcription	HepG2	liver
13	chr2:231237200-231264800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:231240000-231259600	Strong transcription	Primary B cells from cord blood	blood
15	chr2:231244600-231259400	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr2:231244600-231260000	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr2:231244800-231260000	Strong transcription	Primary T cells from cord blood	blood
18	chr2:231244800-231260000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr2:231245000-231260400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr2:231245200-231265600	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr2:231245400-231260400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr2:231245800-231266000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr2:231246400-231260200	Strong transcription	Placenta	Placenta
24	chr2:231247600-231260000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr2:231248000-231260000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr2:231248000-231260000	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr2:231248000-231262600	Strong transcription	Liver	Liver
28	chr2:231248000-231265400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr2:231248000-231274600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr2:231248200-231259400	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr2:231248200-231259600	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr2:231248400-231260800	Strong transcription	Dnd41	blood
33	chr2:231249000-231260000	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr2:231249000-231260600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr2:231249000-231262000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr2:231249000-231273200	Weak transcription	Fetal Muscle Trunk	muscle
37	chr2:231249200-231261800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr2:231249200-231262000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr2:231249400-231260400	Strong transcription	Adipose Nuclei	Adipose
40	chr2:231249400-231260400	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr2:231249400-231262000	Strong transcription	Stomach Smooth Muscle	stomach
42	chr2:231249600-231260600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr2:231249800-231262600	Strong transcription	Duodenum Mucosa	Duodenum
44	chr2:231250200-231273200	Weak transcription	Right Ventricle	heart
45	chr2:231251600-231261400	Strong transcription	HSMM	muscle
46	chr2:231252000-231260600	Weak transcription	Rectal Smooth Muscle	rectum
47	chr2:231252000-231261400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
48	chr2:231252600-231272600	Weak transcription	NHDF-Ad	bronchial
49	chr2:231253200-231259600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:231253200-231260200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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