Variant report

Variant	rs11124669
Chromosome Location	chr2:39494566-39494567
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10185961	0.90[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10865148	0.88[AFR][1000 genomes]
rs11124670	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11124671	0.82[AFR][1000 genomes]
rs11677189	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11677383	0.88[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs11682362	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12151392	0.83[AFR][1000 genomes]
rs12618944	0.83[AFR][1000 genomes]
rs12624242	0.81[AFR][1000 genomes]
rs13002095	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13015356	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2302749	0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2373528	0.81[ASN][1000 genomes]
rs3755171	0.82[AFR][1000 genomes]
rs3755172	0.82[AFR][1000 genomes]
rs3755176	0.82[AFR][1000 genomes]
rs3770671	0.89[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs3770672	0.82[ASN][1000 genomes]
rs3770673	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs3770674	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs62138511	0.85[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6544216	0.89[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs6714566	0.91[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs6753014	0.86[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7569037	0.84[AFR][1000 genomes]
rs7573923	0.88[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7582848	0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7597300	0.81[AFR][1000 genomes]
rs7608958	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 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	nsv2693	chr2:39468641-39513800	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
19	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
20	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
21	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
22	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11124669	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	chr2:39469200-39503800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr2:39469400-39504200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:39471000-39503400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr2:39471200-39503800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr2:39471200-39504200	Weak transcription	Esophagus	oesophagus
6	chr2:39471400-39503400	Weak transcription	Right Ventricle	heart
7	chr2:39472600-39504000	Weak transcription	Thymus	Thymus
8	chr2:39473400-39517400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr2:39474600-39494600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr2:39474600-39494600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:39476200-39502400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr2:39476600-39527600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:39477200-39495200	Strong transcription	Liver	Liver
14	chr2:39477600-39496200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr2:39478600-39543400	Weak transcription	Stomach Mucosa	stomach
16	chr2:39479000-39521200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr2:39479200-39503400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr2:39479600-39494600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr2:39481000-39504200	Weak transcription	Spleen	Spleen
20	chr2:39481000-39580200	Weak transcription	NHEK	skin
21	chr2:39481200-39501800	Weak transcription	Fetal Brain Female	brain
22	chr2:39481200-39503400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr2:39481400-39504000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr2:39481800-39499000	Weak transcription	Brain Substantia Nigra	brain
25	chr2:39481800-39499400	Weak transcription	K562	blood
26	chr2:39481800-39503600	Weak transcription	Brain Anterior Caudate	brain
27	chr2:39481800-39503600	Weak transcription	Colonic Mucosa	Colon
28	chr2:39482000-39502200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr2:39484400-39503400	Weak transcription	Brain Angular Gyrus	brain
30	chr2:39484400-39516400	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr2:39484600-39504000	Weak transcription	Fetal Brain Male	brain
32	chr2:39485200-39503800	Weak transcription	Brain Germinal Matrix	brain
33	chr2:39485200-39504000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:39486000-39503400	Weak transcription	Brain Hippocampus Middle	brain
35	chr2:39486400-39503400	Weak transcription	Fetal Heart	heart
36	chr2:39486600-39503600	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr2:39487400-39499400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr2:39487600-39496800	Weak transcription	HMEC	breast
39	chr2:39487600-39499000	Weak transcription	HUVEC	blood vessel
40	chr2:39487600-39503400	Weak transcription	Lung	lung
41	chr2:39487600-39503400	Weak transcription	Hela-S3	cervix
42	chr2:39487600-39503600	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr2:39487600-39504400	Weak transcription	Gastric	stomach
44	chr2:39487600-39513200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr2:39487800-39495400	Weak transcription	Fetal Stomach	stomach
46	chr2:39487800-39502200	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr2:39487800-39504000	Weak transcription	Aorta	Aorta
48	chr2:39488000-39498600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr2:39488400-39502200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr2:39489800-39496800	Weak transcription	Fetal Lung	lung

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