Variant report

Variant	rs1454220
Chromosome Location	chr2:39277108-39277109
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39276455..39278449-chr2:39282839..39284545,2	K562	blood:

Extended variants
information (count: 125 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10153761	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10166801	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10169337	0.80[CEU][hapmap];0.85[CHB][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10172714	0.85[JPT][hapmap]
rs10177250	0.92[CHB][hapmap]
rs10183915	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs10186762	0.84[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs10192250	0.92[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs10194374	1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10201980	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs10205802	0.80[CEU][hapmap];0.85[CHB][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10206751	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs1043793	0.84[CHB][hapmap]
rs10439459	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11124659	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11124660	0.81[EUR][1000 genomes]
rs11674846	0.85[EUR][1000 genomes]
rs11691035	0.85[EUR][1000 genomes]
rs11692687	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12471731	0.92[CHB][hapmap]
rs12620071	0.83[EUR][1000 genomes]
rs12712630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13023273	0.86[ASN][1000 genomes]
rs1377860	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1377861	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1454219	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1454221	0.83[ASN][1000 genomes]
rs1454222	0.84[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs1454223	0.92[CHB][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs1454225	0.86[ASN][1000 genomes]
rs1454226	1.00[CHB][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1454227	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1454228	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1470915	1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1840281	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1869513	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs1947432	0.86[ASN][1000 genomes]
rs2060987	0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2060988	0.80[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2060989	0.83[EUR][1000 genomes]
rs2123876	0.93[JPT][hapmap];0.86[AMR][1000 genomes]
rs2123879	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2123881	1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2168042	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278914	0.83[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2290445	0.92[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs2305516	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs2373474	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2373495	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2373496	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2373497	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs2888585	0.92[CHB][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2924714	0.83[EUR][1000 genomes]
rs2969763	0.83[EUR][1000 genomes]
rs297121	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs297122	0.83[ASN][1000 genomes]
rs297125	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs297128	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs297129	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs297130	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs297133	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs297135	0.92[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs297137	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs297139	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs297140	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs297141	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs297143	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs297148	0.90[CHB][hapmap];0.84[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs297149	0.92[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs297150	0.92[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes]
rs297153	0.92[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes]
rs297157	0.83[EUR][1000 genomes]
rs297158	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs297159	0.84[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs297160	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs3765058	0.83[CHB][hapmap]
rs378698	0.92[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4142729	0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs422854	0.84[CHB][hapmap];0.80[JPT][hapmap]
rs4643520	0.86[ASN][1000 genomes]
rs4670269	0.83[CHB][hapmap]
rs4670270	0.86[ASN][1000 genomes]
rs4670272	1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4670903	0.84[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs4670905	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4670907	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57378308	0.81[EUR][1000 genomes]
rs59732351	0.81[EUR][1000 genomes]
rs61405040	0.83[EUR][1000 genomes]
rs6544191	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6544194	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6544195	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6544197	1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6704656	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs6713281	1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6716101	0.84[CHB][hapmap]
rs6725356	1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6725644	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6739568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6739807	0.83[EUR][1000 genomes]
rs6752850	0.86[ASN][1000 genomes]
rs6756184	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6758330	0.80[CEU][hapmap];0.85[CHB][hapmap];0.83[EUR][1000 genomes]
rs72909662	0.81[EUR][1000 genomes]
rs7571052	0.83[CHB][hapmap]
rs7577088	0.92[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs7604229	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7607509	0.80[CEU][hapmap];0.85[CHB][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9309031	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs963730	0.91[CHB][hapmap]
rs963731	0.92[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs9679498	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs970409	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs997344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873884	chr2:39154463-39332093	Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv2755359	chr2:39169049-39417849	Strong transcription Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv873885	chr2:39200198-39573521	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1010874	chr2:39255376-39604535	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv535649	chr2:39255376-39604535	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv531346	chr2:39263225-39606367	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
7	nsv533348	chr2:39264345-39596169	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
8	nsv1014520	chr2:39270598-39596299	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
9	nsv535650	chr2:39270598-39596299	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
10	nsv1008198	chr2:39271472-39364035	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
11	nsv1009379	chr2:39271472-39604535	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1454220	SOS1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39213800-39308000	Weak transcription	Pancreas	Pancrea
2	chr2:39227600-39303400	Weak transcription	Colonic Mucosa	Colon
3	chr2:39229800-39293000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:39232600-39300000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:39235400-39312000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:39235600-39293200	Weak transcription	Fetal Brain Male	brain
7	chr2:39235600-39295800	Weak transcription	NHLF	lung
8	chr2:39235600-39298200	Weak transcription	Small Intestine	intestine
9	chr2:39235600-39327800	Weak transcription	Esophagus	oesophagus
10	chr2:39235800-39284000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr2:39235800-39293600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr2:39236000-39295600	Weak transcription	Aorta	Aorta
13	chr2:39236000-39295800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr2:39236000-39305600	Weak transcription	Gastric	stomach
15	chr2:39236200-39305600	Weak transcription	Lung	lung
16	chr2:39240800-39299200	Weak transcription	Brain Hippocampus Middle	brain
17	chr2:39241600-39292800	Weak transcription	GM12878-XiMat	blood
18	chr2:39243200-39299600	Weak transcription	Brain Substantia Nigra	brain
19	chr2:39244600-39295400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr2:39250000-39282200	Weak transcription	Brain Anterior Caudate	brain
21	chr2:39250000-39292800	Weak transcription	Psoas Muscle	Psoas
22	chr2:39250200-39295200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr2:39250200-39313600	Weak transcription	Brain Angular Gyrus	brain
24	chr2:39250400-39295600	Weak transcription	NH-A	brain
25	chr2:39250400-39303000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr2:39250600-39279800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr2:39251000-39293000	Weak transcription	HMEC	breast
28	chr2:39251600-39327200	Weak transcription	HUVEC	blood vessel
29	chr2:39252200-39279200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr2:39252400-39292400	Weak transcription	NHEK	skin
31	chr2:39254200-39277200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr2:39255000-39299000	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr2:39255400-39278200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr2:39255800-39277600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr2:39258200-39277600	Weak transcription	Primary T cells from cord blood	blood
36	chr2:39258200-39293400	Weak transcription	Ovary	ovary
37	chr2:39258400-39282600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr2:39258400-39292800	Weak transcription	HSMMtube	muscle
39	chr2:39258400-39295800	Weak transcription	Colon Smooth Muscle	Colon
40	chr2:39258400-39299200	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr2:39258400-39322400	Weak transcription	Thymus	Thymus
42	chr2:39259000-39293200	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr2:39260000-39277600	Weak transcription	HSMM	muscle
44	chr2:39260200-39278000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr2:39260200-39293000	Weak transcription	Stomach Smooth Muscle	stomach
46	chr2:39260200-39295000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr2:39261000-39277800	Weak transcription	Left Ventricle	heart
48	chr2:39261000-39279600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:39261000-39279600	Weak transcription	Fetal Muscle Leg	muscle
50	chr2:39261000-39309800	Weak transcription	Spleen	Spleen

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