Variant report

Variant	rs2708227
Chromosome Location	chr2:39448453-39448454
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39442096..39444486-chr2:39445586..39448502,3	MCF-7	breast:
2	chr2:39345837..39348382-chr2:39447028..39448859,2	MCF-7	breast:
3	chr2:39441442..39443527-chr2:39448298..39450542,2	K562	blood:

Variant related genes	Relation type
ENSG00000115904	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10199948	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs10490305	1.00[JPT][hapmap]
rs11888511	0.95[EUR][1000 genomes]
rs11898025	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11898704	1.00[JPT][hapmap]
rs17023405	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17023552	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs17023573	0.95[EUR][1000 genomes]
rs17023584	0.95[EUR][1000 genomes]
rs3770661	0.84[EUR][1000 genomes]
rs55797011	0.84[EUR][1000 genomes]
rs55961227	0.84[EUR][1000 genomes]
rs56024079	0.95[EUR][1000 genomes]
rs56361338	0.95[EUR][1000 genomes]
rs56928728	0.84[EUR][1000 genomes]
rs57271382	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57401773	0.95[EUR][1000 genomes]
rs59121834	0.95[EUR][1000 genomes]
rs59707152	0.84[EUR][1000 genomes]
rs61219633	0.84[EUR][1000 genomes]
rs61257289	0.95[EUR][1000 genomes]
rs62138484	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6544201	1.00[AMR][1000 genomes]
rs6544206	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes]
rs6544207	0.84[EUR][1000 genomes]
rs6706379	1.00[AMR][1000 genomes]
rs6710707	1.00[AMR][1000 genomes]
rs6712399	1.00[JPT][hapmap]
rs6715143	1.00[AMR][1000 genomes]
rs6718000	0.84[EUR][1000 genomes]
rs6727395	1.00[JPT][hapmap]
rs6731330	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes]
rs6746820	1.00[AMR][1000 genomes]
rs6755534	0.84[EUR][1000 genomes]
rs6759248	1.00[AMR][1000 genomes]
rs72921023	0.95[EUR][1000 genomes]
rs72927494	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73923836	0.95[EUR][1000 genomes]
rs73923842	0.95[EUR][1000 genomes]
rs73923844	0.84[EUR][1000 genomes]
rs73923847	0.84[EUR][1000 genomes]
rs73923888	0.84[EUR][1000 genomes]
rs73923895	0.84[EUR][1000 genomes]
rs73924815	0.95[EUR][1000 genomes]
rs73924816	0.95[EUR][1000 genomes]
rs73924817	0.95[EUR][1000 genomes]
rs73930526	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73930538	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7563373	1.00[CEU][hapmap]
rs7569943	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7584699	1.00[AMR][1000 genomes]
rs7588265	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7588424	1.00[AMR][1000 genomes]
rs7589576	1.00[AMR][1000 genomes]
rs7589697	1.00[AMR][1000 genomes]
rs7591563	0.84[EUR][1000 genomes]
rs7595047	0.84[EUR][1000 genomes]
rs7595102	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes]
rs7596222	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7596255	1.00[AMR][1000 genomes]
rs7599017	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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
19	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2708227	SOS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39419000-39455600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr2:39423400-39470800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:39429800-39459600	Weak transcription	HSMM	muscle
4	chr2:39431600-39455000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:39431800-39455200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr2:39435400-39455600	Weak transcription	Left Ventricle	heart
7	chr2:39439400-39455200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr2:39442600-39455000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr2:39443800-39455000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr2:39444000-39452800	Weak transcription	Pancreas	Pancrea
11	chr2:39445600-39448800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr2:39445600-39450400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr2:39445800-39453800	Weak transcription	Lung	lung
14	chr2:39447000-39454600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr2:39447200-39455000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr2:39447400-39448800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr2:39447400-39453800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr2:39447600-39448800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr2:39447600-39449000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr2:39447600-39453800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr2:39447600-39454800	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr2:39447600-39454800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr2:39447600-39455000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr2:39447600-39456400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:39448400-39449200	Enhancers	HepG2	liver
26	chr2:39448400-39449200	Strong transcription	HSMMtube	muscle

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