Variant report

Variant	rs58645871
Chromosome Location	chr2:39352611-39352612
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NRF1	chr2:39350886-39352866	SK-N-SH	brain:	n/a	chr2:39351640-39351649 chr2:39351465-39351476 chr2:39351451-39351462 chr2:39351465-39351479 chr2:39351464-39351475
2	CUX1	chr2:39352568-39352744	GM12878	blood:	n/a	n/a
3	CUX1	chr2:39352452-39352939	K562	blood:	n/a	n/a
4	GATA1	chr2:39350841-39352807	PBDE	blood:	n/a	n/a
5	JUN	chr2:39350696-39352726	K562	blood:	n/a	chr2:39352313-39352323

No.	Distal block	Cell Line	Cell type
1	chr2:39350652..39354915-chr2:39355009..39358498,5	K562	blood:
2	chr2:39350652..39353712-chr2:39355009..39357216,3	K562	blood:
3	chr2:39053934..39056407-chr2:39351577..39353846,2	K562	blood:
4	chr2:39351946..39354916-chr2:39358761..39361361,2	K562	blood:

Variant related genes	Relation type
SOS1	TF binding region
ENSG00000202309	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10153761	0.89[EUR][1000 genomes]
rs10165968	0.80[EUR][1000 genomes]
rs10166801	0.87[EUR][1000 genomes]
rs10172085	0.83[EUR][1000 genomes]
rs10183915	1.00[AFR][1000 genomes]
rs10194374	0.87[EUR][1000 genomes]
rs10439459	0.89[EUR][1000 genomes]
rs11124659	0.89[EUR][1000 genomes]
rs11124660	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11692687	0.89[EUR][1000 genomes]
rs12620003	0.80[EUR][1000 genomes]
rs12620071	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1377860	0.93[EUR][1000 genomes]
rs1377861	0.93[EUR][1000 genomes]
rs1377863	0.85[EUR][1000 genomes]
rs1454226	0.89[EUR][1000 genomes]
rs1454228	0.83[EUR][1000 genomes]
rs1470915	0.89[EUR][1000 genomes]
rs1840281	0.83[EUR][1000 genomes]
rs2060989	0.93[EUR][1000 genomes]
rs2123876	0.85[EUR][1000 genomes]
rs2123879	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2123881	0.89[EUR][1000 genomes]
rs2373474	0.87[EUR][1000 genomes]
rs2373495	0.85[EUR][1000 genomes]
rs2373496	0.85[EUR][1000 genomes]
rs2888585	0.89[EUR][1000 genomes]
rs2924714	0.93[EUR][1000 genomes]
rs2969763	0.93[EUR][1000 genomes]
rs297121	0.93[EUR][1000 genomes]
rs297125	0.93[EUR][1000 genomes]
rs297128	0.93[EUR][1000 genomes]
rs297129	0.93[EUR][1000 genomes]
rs297130	0.93[EUR][1000 genomes]
rs297133	0.93[EUR][1000 genomes]
rs297135	0.93[EUR][1000 genomes]
rs297137	0.93[EUR][1000 genomes]
rs297139	0.93[EUR][1000 genomes]
rs297140	0.93[EUR][1000 genomes]
rs297141	0.93[EUR][1000 genomes]
rs297143	0.93[EUR][1000 genomes]
rs297148	0.93[EUR][1000 genomes]
rs297149	0.93[EUR][1000 genomes]
rs297150	0.93[EUR][1000 genomes]
rs297151	0.80[EUR][1000 genomes]
rs297152	0.80[EUR][1000 genomes]
rs297153	0.93[EUR][1000 genomes]
rs297156	0.80[EUR][1000 genomes]
rs297157	0.93[EUR][1000 genomes]
rs297158	0.91[EUR][1000 genomes]
rs297159	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs378698	0.93[EUR][1000 genomes]
rs4670272	0.85[EUR][1000 genomes]
rs4670905	0.93[EUR][1000 genomes]
rs4670907	0.82[EUR][1000 genomes]
rs57378308	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59732351	0.91[EUR][1000 genomes]
rs61405040	0.93[EUR][1000 genomes]
rs6544191	0.93[EUR][1000 genomes]
rs6544194	0.80[EUR][1000 genomes]
rs6544195	0.80[EUR][1000 genomes]
rs6544197	0.93[EUR][1000 genomes]
rs6713281	0.89[EUR][1000 genomes]
rs6725356	0.87[EUR][1000 genomes]
rs6725644	0.87[EUR][1000 genomes]
rs6756184	0.85[EUR][1000 genomes]
rs72909662	0.91[EUR][1000 genomes]
rs7568552	0.87[EUR][1000 genomes]
rs9309031	0.84[EUR][1000 genomes]
rs970409	0.93[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
rs58645871	SOS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39350400-39353000	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr2:39350600-39352800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:39350600-39352800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr2:39350800-39352800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr2:39352000-39352800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
6	chr2:39352000-39352800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr2:39352000-39352800	Flanking Active TSS	Adipose Nuclei	Adipose
8	chr2:39352200-39352800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr2:39352200-39352800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr2:39352200-39352800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr2:39352200-39352800	Flanking Active TSS	A549	lung
12	chr2:39352200-39352800	Flanking Active TSS	Dnd41	blood
13	chr2:39352200-39352800	Flanking Active TSS	HepG2	liver
14	chr2:39352200-39352800	Flanking Active TSS	K562	blood
15	chr2:39352200-39353000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:39352400-39352800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr2:39352400-39352800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:39352400-39352800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr2:39352400-39352800	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr2:39352400-39352800	Enhancers	Primary B cells from peripheral blood	blood
21	chr2:39352400-39352800	Enhancers	Primary T cells from cord blood	blood
22	chr2:39352400-39352800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr2:39352400-39352800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr2:39352400-39352800	Enhancers	Fetal Intestine Large	intestine
25	chr2:39352400-39352800	Enhancers	Stomach Mucosa	stomach
26	chr2:39352400-39352800	Flanking Active TSS	NHDF-Ad	bronchial
27	chr2:39352400-39353000	Enhancers	Fetal Intestine Small	intestine
28	chr2:39352400-39354400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr2:39352400-39355000	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr2:39352400-39355000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr2:39352400-39355200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr2:39352400-39356800	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr2:39352600-39352800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:39352600-39352800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr2:39352600-39352800	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr2:39352600-39352800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr2:39352600-39352800	Enhancers	Primary B cells from cord blood	blood
38	chr2:39352600-39352800	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr2:39352600-39352800	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr2:39352600-39352800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr2:39352600-39352800	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr2:39352600-39352800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr2:39352600-39352800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr2:39352600-39352800	Enhancers	Liver	Liver
45	chr2:39352600-39352800	Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr2:39352600-39352800	Enhancers	Fetal Heart	heart
47	chr2:39352600-39352800	Enhancers	Fetal Stomach	stomach
48	chr2:39352600-39352800	Active TSS	Thymus	Thymus
49	chr2:39352600-39352800	Enhancers	GM12878-XiMat	blood
50	chr2:39352600-39352800	Enhancers	Hela-S3	cervix

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