Variant report

Variant	rs3755172
Chromosome Location	chr2:39514136-39514137
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1012689	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10166473	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs10168941	0.89[AMR][1000 genomes]
rs10169329	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs10179936	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs10185961	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10193636	0.83[AFR][1000 genomes]
rs10193807	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10865148	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11124667	0.82[ASN][1000 genomes]
rs11124669	0.82[AFR][1000 genomes]
rs11124670	0.82[AFR][1000 genomes]
rs11124671	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11124672	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs11124674	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11124675	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs11124678	0.89[AFR][1000 genomes]
rs11124680	0.82[ASN][1000 genomes]
rs11677383	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11677611	0.82[ASN][1000 genomes]
rs11688033	0.95[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12151392	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12162306	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12618944	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12624242	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12712634	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12712640	0.85[ASN][1000 genomes]
rs12712642	0.82[ASN][1000 genomes]
rs12997072	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13002095	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs13015356	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13405577	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1861733	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1861734	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2024514	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2058863	0.89[AFR][1000 genomes]
rs2302749	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2373528	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2888593	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3755171	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3755176	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3770662	0.81[ASN][1000 genomes]
rs3770663	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs3770664	0.85[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3770671	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3770672	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3770673	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3770674	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4488638	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62138511	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6544214	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6544215	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6544216	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6709424	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6714566	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6719469	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6725790	0.85[AMR][1000 genomes]
rs6753014	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7340455	0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7421175	0.82[ASN][1000 genomes]
rs7425616	0.82[AMR][1000 genomes]
rs7559752	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs7559756	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs7561630	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7569037	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7569492	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7573923	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7581692	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7582848	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7594145	0.84[ASN][1000 genomes]
rs7595469	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7597300	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7600636	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs7605427	0.93[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7608958	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9037	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9309036	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9309037	0.92[AFR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9309038	0.91[AFR][1000 genomes]
rs9309039	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	esv1832414	chr2:39385155-39588797	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	esv1827292	chr2:39385155-39675339	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
14	esv1812828	chr2:39396457-39675339	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
15	nsv833847	chr2:39410762-39604640	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	nsv533445	chr2:39412970-39605266	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
17	esv1830024	chr2:39440552-39588797	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
18	nsv873886	chr2:39468676-39573521	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	nsv873887	chr2:39468676-39601889	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
20	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
21	esv1809158	chr2:39474679-39588797	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
22	esv1828851	chr2:39508121-39588797	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
23	nsv873888	chr2:39508830-39573521	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3755172	SOS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39473400-39517400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:39476600-39527600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:39478600-39543400	Weak transcription	Stomach Mucosa	stomach
4	chr2:39479000-39521200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr2:39481000-39580200	Weak transcription	NHEK	skin
6	chr2:39484400-39516400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr2:39493600-39523800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr2:39493600-39565800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr2:39493800-39516600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr2:39493800-39525000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr2:39494000-39525600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr2:39494000-39553000	Weak transcription	GM12878-XiMat	blood
13	chr2:39495600-39523200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr2:39496400-39521200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:39496600-39515000	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr2:39496600-39520400	Strong transcription	Placenta	Placenta
17	chr2:39497000-39516600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:39497200-39516000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr2:39504400-39521400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:39504600-39515000	Weak transcription	Brain Cingulate Gyrus	brain
21	chr2:39504600-39523600	Weak transcription	Brain Substantia Nigra	brain
22	chr2:39504600-39540000	Weak transcription	Right Ventricle	heart
23	chr2:39504600-39562000	Weak transcription	Psoas Muscle	Psoas
24	chr2:39504800-39518400	Weak transcription	Esophagus	oesophagus
25	chr2:39504800-39518800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr2:39504800-39521800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr2:39504800-39527800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr2:39504800-39538400	Weak transcription	Small Intestine	intestine
29	chr2:39504800-39541600	Weak transcription	Fetal Brain Male	brain
30	chr2:39504800-39565800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr2:39504800-39567200	Weak transcription	Hela-S3	cervix
32	chr2:39505000-39518600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr2:39505000-39523400	Weak transcription	Brain Germinal Matrix	brain
34	chr2:39505000-39527400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr2:39505000-39538200	Weak transcription	Lung	lung
36	chr2:39505200-39518400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr2:39505400-39517600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr2:39505400-39518000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr2:39505400-39519400	Weak transcription	Spleen	Spleen
40	chr2:39505400-39556800	Weak transcription	Thymus	Thymus
41	chr2:39505400-39557200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr2:39505400-39562400	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr2:39505600-39515000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr2:39505600-39540000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr2:39506000-39518800	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr2:39507000-39517800	Weak transcription	Fetal Thymus	thymus
47	chr2:39507200-39538400	Weak transcription	Aorta	Aorta
48	chr2:39507600-39522200	Strong transcription	HSMM	muscle
49	chr2:39508000-39521000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr2:39508600-39515800	Strong transcription	Adipose Nuclei	Adipose

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