Variant report

Variant	rs11124668
Chromosome Location	chr2:39482087-39482088
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39476355..39478295-chr2:39480403..39482715,2	MCF-7	breast:
2	chr2:39476438..39480963-chr2:39481034..39484561,4	K562	blood:

Extended variants
information (count: 99 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10153665	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs10170424	0.85[EUR][1000 genomes]
rs10170617	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10172736	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10173556	0.89[EUR][1000 genomes]
rs10175038	1.00[EUR][1000 genomes]
rs10175333	0.84[YRI][hapmap]
rs10190069	0.81[EUR][1000 genomes]
rs10193636	0.88[CHB][hapmap]
rs10195629	0.96[EUR][1000 genomes]
rs1035232	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs10427162	0.84[JPT][hapmap]
rs10865149	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10865150	0.82[CEU][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10865152	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs11124673	0.85[EUR][1000 genomes]
rs11124676	1.00[CEU][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11124677	0.80[AFR][1000 genomes]
rs11124679	0.86[EUR][1000 genomes]
rs1125839	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1211996	0.87[EUR][1000 genomes]
rs12622941	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs12712636	0.83[ASN][1000 genomes]
rs1468902	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17023837	0.83[EUR][1000 genomes]
rs1861735	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1922827	1.00[CEU][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2005892	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2111382	0.87[AFR][1000 genomes]
rs2178760	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2178762	0.86[EUR][1000 genomes]
rs2193422	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2373534	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2373535	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs2373536	0.84[YRI][hapmap]
rs2542008	0.88[EUR][1000 genomes]
rs2888594	0.86[EUR][1000 genomes]
rs2888598	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs3755177	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3755178	1.00[CEU][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3770663	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs3770670	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3770675	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3770678	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3815594	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs4670935	0.84[YRI][hapmap]
rs6544213	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6544220	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6544222	0.90[EUR][1000 genomes]
rs6544224	0.87[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.84[EUR][1000 genomes]
rs6712274	0.86[EUR][1000 genomes]
rs6712921	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6718134	0.88[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs6725790	0.80[ASN][1000 genomes]
rs6725938	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6732611	0.83[EUR][1000 genomes]
rs6736700	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6741019	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6742170	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6743041	1.00[CEU][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6753323	0.85[EUR][1000 genomes]
rs6756183	1.00[CEU][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6760382	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs7573535	0.86[CHB][hapmap]
rs7574250	0.81[AMR][1000 genomes]
rs7578136	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7579414	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7582160	0.89[YRI][hapmap]
rs759589	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7600014	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7600046	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7601700	1.00[CEU][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7603337	0.90[EUR][1000 genomes]
rs7603392	0.84[YRI][hapmap]
rs7604047	0.82[EUR][1000 genomes]
rs7608153	0.84[EUR][1000 genomes]
rs9309039	0.90[CHB][hapmap]

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
rs11124668	SOS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 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	chr2:39471200-39483800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:39471200-39503800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:39471200-39504200	Weak transcription	Esophagus	oesophagus
7	chr2:39471400-39503400	Weak transcription	Right Ventricle	heart
8	chr2:39472600-39504000	Weak transcription	Thymus	Thymus
9	chr2:39472800-39492000	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr2:39473000-39482600	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr2:39473000-39485600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr2:39473000-39491000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr2:39473000-39492200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr2:39473200-39491400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr2:39473400-39517400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr2:39474600-39482400	Strong transcription	HSMM	muscle
17	chr2:39474600-39492600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr2:39474600-39494600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr2:39474600-39494600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr2:39474800-39492600	Weak transcription	Psoas Muscle	Psoas
21	chr2:39475000-39483000	Strong transcription	NH-A	brain
22	chr2:39475600-39493600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr2:39475600-39494200	Strong transcription	Placenta	Placenta
24	chr2:39475600-39494400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr2:39475800-39482200	Strong transcription	Adipose Nuclei	Adipose
26	chr2:39476200-39483800	Weak transcription	Hela-S3	cervix
27	chr2:39476200-39502400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr2:39476400-39484600	Strong transcription	HepG2	liver
29	chr2:39476600-39527600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:39476800-39483800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr2:39477000-39487800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr2:39477200-39495200	Strong transcription	Liver	Liver
33	chr2:39477400-39482200	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr2:39477400-39482800	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr2:39477600-39483000	Strong transcription	HSMMtube	muscle
36	chr2:39477600-39484400	Strong transcription	Fetal Kidney	kidney
37	chr2:39477600-39487800	Strong transcription	Fetal Muscle Leg	muscle
38	chr2:39477600-39487800	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr2:39477600-39488400	Strong transcription	Fetal Muscle Trunk	muscle
40	chr2:39477600-39489800	Strong transcription	Fetal Lung	lung
41	chr2:39477600-39492200	Strong transcription	Osteobl	bone
42	chr2:39477600-39496200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr2:39477800-39488600	Strong transcription	Fetal Intestine Large	intestine
44	chr2:39477800-39493200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr2:39478400-39482400	Strong transcription	Primary hematopoietic stem cells	blood
46	chr2:39478400-39487200	Weak transcription	Gastric	stomach
47	chr2:39478400-39491600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr2:39478600-39543400	Weak transcription	Stomach Mucosa	stomach
49	chr2:39478800-39487800	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr2:39479000-39492000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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