Variant report

Variant	rs12620071
Chromosome Location	chr2:39345873-39345874
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38976752..38978404-chr2:39344867..39346987,2	K562	blood:
2	chr2:39319265..39325749-chr2:39345590..39349573,11	MCF-7	breast:
3	chr2:39342488..39346158-chr2:39346528..39349240,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115904	Chromatin interaction
ENSG00000115875	Chromatin interaction
ENSG00000225900	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10153761	0.96[EUR][1000 genomes]
rs10165968	0.87[EUR][1000 genomes]
rs10166801	0.94[EUR][1000 genomes]
rs10172085	0.91[EUR][1000 genomes]
rs10177250	0.83[EUR][1000 genomes]
rs10190377	0.82[EUR][1000 genomes]
rs10194374	0.94[EUR][1000 genomes]
rs10200058	0.82[EUR][1000 genomes]
rs10201980	0.85[JPT][hapmap]
rs10439459	0.96[EUR][1000 genomes]
rs11124659	0.96[EUR][1000 genomes]
rs11124660	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11692687	0.96[EUR][1000 genomes]
rs12620003	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12622969	0.85[EUR][1000 genomes]
rs12712630	0.83[EUR][1000 genomes]
rs13033392	0.82[EUR][1000 genomes]
rs1377860	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1377861	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1377863	0.93[EUR][1000 genomes]
rs1454220	0.83[EUR][1000 genomes]
rs1454226	0.96[EUR][1000 genomes]
rs1454227	0.84[EUR][1000 genomes]
rs1454228	0.91[EUR][1000 genomes]
rs1470914	0.80[EUR][1000 genomes]
rs1470915	0.96[EUR][1000 genomes]
rs1840281	0.91[EUR][1000 genomes]
rs2060989	1.00[EUR][1000 genomes]
rs2123876	0.93[EUR][1000 genomes]
rs2123879	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2123881	0.96[EUR][1000 genomes]
rs2168042	0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs2305516	0.85[JPT][hapmap]
rs2373474	0.94[EUR][1000 genomes]
rs2373495	0.93[EUR][1000 genomes]
rs2373496	0.93[EUR][1000 genomes]
rs2888585	0.96[EUR][1000 genomes]
rs2924714	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2969763	1.00[EUR][1000 genomes]
rs297120	0.81[EUR][1000 genomes]
rs297121	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs297122	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs297124	0.83[EUR][1000 genomes]
rs297125	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs297127	0.83[EUR][1000 genomes]
rs297128	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs297129	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs297130	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs297131	0.84[EUR][1000 genomes]
rs297132	0.85[EUR][1000 genomes]
rs297133	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs297134	0.85[EUR][1000 genomes]
rs297135	0.86[JPT][hapmap];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs297136	0.85[EUR][1000 genomes]
rs297137	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs297139	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs297140	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs297141	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs297142	0.85[EUR][1000 genomes]
rs297143	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs297144	0.83[EUR][1000 genomes]
rs297145	0.85[EUR][1000 genomes]
rs297147	0.85[EUR][1000 genomes]
rs297148	1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs297149	1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs297150	0.85[JPT][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs297151	0.87[EUR][1000 genomes]
rs297152	0.87[EUR][1000 genomes]
rs297153	0.92[JPT][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs297155	0.80[EUR][1000 genomes]
rs297156	0.87[EUR][1000 genomes]
rs297157	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs297158	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs297159	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs297160	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs297161	0.83[EUR][1000 genomes]
rs366840	0.85[EUR][1000 genomes]
rs378698	0.86[JPT][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3796038	0.80[EUR][1000 genomes]
rs388958	0.85[EUR][1000 genomes]
rs4670272	0.93[EUR][1000 genomes]
rs4670903	0.81[JPT][hapmap]
rs4670905	1.00[EUR][1000 genomes]
rs57378308	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58645871	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59732351	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61405040	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6419600	0.85[EUR][1000 genomes]
rs6544191	1.00[EUR][1000 genomes]
rs6544194	0.87[EUR][1000 genomes]
rs6544195	0.87[EUR][1000 genomes]
rs6544197	0.91[JPT][hapmap];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6713281	0.96[EUR][1000 genomes]
rs6725356	0.94[EUR][1000 genomes]
rs6725644	0.94[EUR][1000 genomes]
rs6726833	0.82[EUR][1000 genomes]
rs6739568	0.83[EUR][1000 genomes]
rs6756184	0.93[EUR][1000 genomes]
rs72909662	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7568552	0.91[EUR][1000 genomes]
rs9309031	0.91[EUR][1000 genomes]
rs970409	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs997344	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755359	chr2:39169049-39417849	Strong transcription Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	nsv1008198	chr2:39271472-39364035	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
10	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
11	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
12	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
13	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
14	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12620071	SOS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39328000-39346800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:39330000-39346800	Weak transcription	Spleen	Spleen
3	chr2:39334600-39346000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:39334600-39346800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:39339800-39346800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:39339800-39346800	Weak transcription	Esophagus	oesophagus
7	chr2:39339800-39346800	Weak transcription	Lung	lung
8	chr2:39340000-39346000	Weak transcription	Placenta	Placenta
9	chr2:39340600-39346000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr2:39342400-39346800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:39343000-39346800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:39343400-39346000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr2:39344400-39346000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
14	chr2:39344400-39346000	Enhancers	Small Intestine	intestine
15	chr2:39344400-39348600	Active TSS	GM12878-XiMat	blood
16	chr2:39344600-39346000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr2:39344600-39346000	Enhancers	Thymus	Thymus
18	chr2:39344800-39346000	Enhancers	Brain Hippocampus Middle	brain
19	chr2:39344800-39346000	Enhancers	Stomach Mucosa	stomach
20	chr2:39345000-39346000	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr2:39345000-39346000	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr2:39345000-39346000	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr2:39345000-39346000	Flanking Active TSS	HepG2	liver
24	chr2:39345000-39347200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr2:39345000-39347200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr2:39345000-39347200	Flanking Active TSS	Adipose Nuclei	Adipose
27	chr2:39345000-39347200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr2:39345200-39346000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr2:39345200-39346000	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr2:39345200-39346000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:39345200-39346000	Enhancers	Primary B cells from peripheral blood	blood
32	chr2:39345200-39346000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr2:39345200-39346000	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr2:39345200-39346000	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr2:39345200-39346200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr2:39345200-39346200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr2:39345200-39346200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
38	chr2:39345200-39346200	Flanking Active TSS	Duodenum Mucosa	Duodenum
39	chr2:39345200-39346200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr2:39345200-39346200	Flanking Active TSS	Fetal Lung	lung
41	chr2:39345200-39346200	Flanking Active TSS	Hela-S3	cervix
42	chr2:39345200-39346400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr2:39345200-39346400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr2:39345200-39346400	Flanking Active TSS	Fetal Heart	heart
45	chr2:39345200-39346800	Flanking Active TSS	Fetal Brain Female	brain
46	chr2:39345200-39347400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
47	chr2:39345200-39348800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr2:39345400-39346000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
49	chr2:39345400-39346000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr2:39345400-39346000	Enhancers	Brain Cingulate Gyrus	brain

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