Variant report

Variant	rs7563858
Chromosome Location	chr2:39430919-39430920
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10174268	0.84[AMR][1000 genomes]
rs10178527	0.88[ASN][1000 genomes]
rs10199708	0.84[AMR][1000 genomes]
rs10865146	0.98[EUR][1000 genomes]
rs10865147	0.81[ASN][1000 genomes]
rs11124661	0.92[EUR][1000 genomes]
rs11124663	0.95[EUR][1000 genomes]
rs11673802	1.00[EUR][1000 genomes]
rs11677985	0.94[EUR][1000 genomes]
rs11689688	1.00[EUR][1000 genomes]
rs12165133	0.92[EUR][1000 genomes]
rs12712631	0.83[EUR][1000 genomes]
rs13005378	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13028683	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1548170	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1976594	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2136638	0.92[EUR][1000 genomes]
rs2373527	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2708222	0.90[ASN][1000 genomes]
rs2708223	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4670917	0.91[EUR][1000 genomes]
rs6544209	0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6544210	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6544211	0.91[EUR][1000 genomes]
rs6753194	0.92[EUR][1000 genomes]
rs6759501	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6761679	1.00[EUR][1000 genomes]
rs7562981	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7563373	0.92[EUR][1000 genomes]
rs7569834	0.84[AMR][1000 genomes]
rs7573535	0.95[EUR][1000 genomes]
rs7583170	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7584676	1.00[EUR][1000 genomes]
rs7590889	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7594004	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7596120	0.81[EUR][1000 genomes]
rs7607761	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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	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
13	nsv1000658	chr2:39374206-39466374	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
14	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
15	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
16	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
17	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
18	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7563858	SOS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39411000-39448400	Weak transcription	HSMMtube	muscle
2	chr2:39419000-39455600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:39423400-39470800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:39429400-39431400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr2:39429600-39431800	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr2:39429800-39431000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:39429800-39431000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr2:39429800-39431200	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr2:39429800-39459600	Weak transcription	HSMM	muscle
10	chr2:39430000-39431000	Enhancers	H9 Cell Line	embryonic stem cell
11	chr2:39430000-39431200	Enhancers	H1 Cell Line	embryonic stem cell
12	chr2:39430000-39431200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:39430000-39431600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:39430000-39431600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr2:39430200-39431400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr2:39430200-39431800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
17	chr2:39430400-39431000	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr2:39430400-39431200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr2:39430400-39431400	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr2:39430400-39431600	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr2:39430400-39431800	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr2:39430600-39431400	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr2:39430600-39431800	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr2:39430800-39431200	Enhancers	Primary T cells from cord blood	blood
25	chr2:39430800-39431600	Enhancers	Breast Myoepithelial Primary Cells	Breast

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