Variant report

Variant	rs2060988
Chromosome Location	chr2:39282684-39282685
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 122 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10165968	0.80[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap];0.82[EUR][1000 genomes]
rs10166395	0.80[CEU][hapmap]
rs10166631	0.82[ASN][1000 genomes]
rs10166801	0.85[CHB][hapmap];0.93[JPT][hapmap]
rs10169337	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10172085	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10177250	0.80[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10183915	0.86[JPT][hapmap]
rs10184015	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10186762	0.86[JPT][hapmap]
rs10190377	0.80[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10192250	0.86[JPT][hapmap]
rs10194374	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs10200058	0.80[EUR][1000 genomes]
rs10201980	0.80[GIH][hapmap];0.86[JPT][hapmap]
rs10205802	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10206751	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1037495	0.80[CEU][hapmap];0.92[CHB][hapmap]
rs1043793	0.80[CEU][hapmap];0.83[GIH][hapmap]
rs11674846	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11691035	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12471731	0.80[CEU][hapmap];0.86[GIH][hapmap];0.89[TSI][hapmap]
rs12620003	0.89[CHB][hapmap];0.82[EUR][1000 genomes]
rs12622969	0.80[CEU][hapmap];0.92[CHB][hapmap];0.83[EUR][1000 genomes]
rs12712630	0.80[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13031871	0.86[CHB][hapmap];0.80[CHD][hapmap];0.90[GIH][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13033392	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1377860	0.83[CHB][hapmap];0.90[CHD][hapmap];0.93[JPT][hapmap]
rs1377863	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1377864	0.80[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1454219	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1454220	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1454223	0.83[GIH][hapmap];0.86[JPT][hapmap]
rs1454226	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs1454227	0.82[EUR][1000 genomes]
rs1470914	0.80[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1470915	0.85[CHB][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap]
rs1869513	0.80[GIH][hapmap]
rs2060987	0.90[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap]
rs2060989	0.88[ASN][1000 genomes]
rs2123876	0.86[JPT][hapmap]
rs2123879	0.83[CHB][hapmap];0.92[JPT][hapmap]
rs2123881	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs2123882	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2168042	0.80[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2168043	0.93[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap]
rs2278914	0.93[JPT][hapmap]
rs2290445	0.86[JPT][hapmap]
rs2305516	0.83[GIH][hapmap];0.86[JPT][hapmap]
rs2373495	0.85[CHB][hapmap];0.93[JPT][hapmap]
rs2373496	0.83[CHB][hapmap];0.92[JPT][hapmap]
rs2373497	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2888585	0.85[CHB][hapmap]
rs297120	0.93[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs297124	1.00[ASW][hapmap];0.80[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.94[LWK][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.83[YRI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs297127	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs297131	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs297132	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs297134	0.80[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs297135	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs297136	0.80[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs297142	0.93[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.88[LWK][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs297144	0.80[CEU][hapmap];1.00[CHB][hapmap];0.97[YRI][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs297145	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs297147	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs297148	0.81[CHB][hapmap]
rs297149	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs297150	0.85[CHB][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap]
rs297151	1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs297152	1.00[CHB][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs297153	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs297155	0.84[ASN][1000 genomes]
rs297156	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs297158	0.85[CHB][hapmap];0.93[JPT][hapmap]
rs297160	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs297161	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs366840	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3765058	0.86[GIH][hapmap]
rs378698	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs3796038	0.80[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs388958	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4142729	0.93[JPT][hapmap]
rs4670269	0.83[GIH][hapmap]
rs4670272	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs4670902	0.80[CEU][hapmap];0.92[CHB][hapmap];0.82[ASN][1000 genomes]
rs6419600	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs6544183	0.83[GIH][hapmap]
rs6544185	0.86[GIH][hapmap]
rs6544188	0.87[ASN][1000 genomes]
rs6544189	0.84[ASN][1000 genomes]
rs6544194	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6544195	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6544197	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs6713281	0.85[CHB][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap]
rs6725356	0.85[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap]
rs6739568	0.80[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6739807	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6756184	0.85[CHB][hapmap];0.93[JPT][hapmap]
rs6758330	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7571052	0.86[GIH][hapmap]
rs7577088	0.90[GIH][hapmap];0.86[JPT][hapmap]
rs7604229	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7607509	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs963730	0.80[CEU][hapmap]
rs963731	0.86[JPT][hapmap]
rs9679498	0.86[JPT][hapmap]
rs997344	0.80[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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
12	nsv581493	chr2:39277851-39547575	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
13	nsv581494	chr2:39277851-39626388	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
14	nsv533456	chr2:39281834-39596298	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
15	nsv581495	chr2:39282079-39475205	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2060988	SOS1	cis	multi-tissue	Pritchard
rs2060988	SOS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 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	chr2:39250000-39292800	Weak transcription	Psoas Muscle	Psoas
21	chr2:39250200-39295200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr2:39250200-39313600	Weak transcription	Brain Angular Gyrus	brain
23	chr2:39250400-39295600	Weak transcription	NH-A	brain
24	chr2:39250400-39303000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr2:39251000-39293000	Weak transcription	HMEC	breast
26	chr2:39251600-39327200	Weak transcription	HUVEC	blood vessel
27	chr2:39252400-39292400	Weak transcription	NHEK	skin
28	chr2:39255000-39299000	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr2:39258200-39293400	Weak transcription	Ovary	ovary
30	chr2:39258400-39292800	Weak transcription	HSMMtube	muscle
31	chr2:39258400-39295800	Weak transcription	Colon Smooth Muscle	Colon
32	chr2:39258400-39299200	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr2:39258400-39322400	Weak transcription	Thymus	Thymus
34	chr2:39259000-39293200	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr2:39260200-39293000	Weak transcription	Stomach Smooth Muscle	stomach
36	chr2:39260200-39295000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr2:39261000-39309800	Weak transcription	Spleen	Spleen
38	chr2:39261000-39318800	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr2:39261000-39327800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr2:39262000-39292600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr2:39270600-39284400	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr2:39271400-39320400	Weak transcription	Right Ventricle	heart
43	chr2:39272800-39310200	Weak transcription	Fetal Heart	heart
44	chr2:39274000-39284000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:39274000-39284000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr2:39274000-39284800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr2:39274200-39284600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr2:39274400-39283000	Strong transcription	Adipose Nuclei	Adipose
49	chr2:39274600-39283600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr2:39275200-39283200	Strong transcription	Primary monocytes fromperipheralblood	blood

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