Variant report

Variant	rs3099947
Chromosome Location	chr2:39108387-39108388
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39106547..39110069-chr2:39150032..39154401,3	K562	blood:
2	chr2:39106402..39108515-chr2:39149048..39151113,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10165289	1.00[CEU][hapmap]
rs10186448	1.00[CEU][hapmap]
rs10186842	1.00[CEU][hapmap]
rs13421894	1.00[CEU][hapmap]
rs1376461	1.00[JPT][hapmap]
rs1451278	1.00[CEU][hapmap]
rs17023042	1.00[CEU][hapmap]
rs17023045	1.00[CEU][hapmap]
rs17023149	1.00[CEU][hapmap]
rs17023214	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs17023241	1.00[CEU][hapmap]
rs17023292	1.00[CEU][hapmap]
rs17425982	1.00[CEU][hapmap]
rs1901290	1.00[CEU][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2373466	1.00[CEU][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2373472	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs3099938	1.00[CEU][hapmap]
rs3099953	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3099973	1.00[CEU][hapmap]
rs3099997	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3112138	1.00[JPT][hapmap]
rs3112157	1.00[CEU][hapmap]
rs3112158	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs3112160	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs3112164	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3112174	0.99[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3112176	1.00[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3112177	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs56322480	0.92[ASN][1000 genomes]
rs57884089	0.85[ASN][1000 genomes]
rs58412684	0.92[ASN][1000 genomes]
rs58645810	0.92[ASN][1000 genomes]
rs59788371	0.92[ASN][1000 genomes]
rs60406386	0.92[ASN][1000 genomes]
rs61393528	0.92[ASN][1000 genomes]
rs6544182	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6712917	1.00[JPT][hapmap]
rs6722176	0.92[ASN][1000 genomes]
rs6722478	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6748000	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7368897	1.00[JPT][hapmap]
rs73930373	0.92[ASN][1000 genomes]
rs73930374	0.92[ASN][1000 genomes]
rs73930378	0.92[ASN][1000 genomes]
rs7565814	1.00[CEU][hapmap]
rs7571935	0.92[ASN][1000 genomes]
rs7583010	1.00[CEU][hapmap]
rs7599990	1.00[CEU][hapmap]
rs7605183	0.92[ASN][1000 genomes]
rs921433	1.00[JPT][hapmap]
rs9678084	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv2692	chr2:39065768-39111871	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	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
rs3099947	SOS1	cis	multi-tissue	Pritchard

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39103800-39113400	Weak transcription	Pancreas	Pancrea
2	chr2:39103800-39113400	Weak transcription	HSMMtube	muscle
3	chr2:39103800-39114000	Weak transcription	Lung	lung
4	chr2:39103800-39120200	Weak transcription	Left Ventricle	heart
5	chr2:39104000-39111200	Weak transcription	HUVEC	blood vessel
6	chr2:39104000-39112600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr2:39104000-39112600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr2:39104000-39113200	Weak transcription	Right Ventricle	heart
9	chr2:39104000-39113400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr2:39104000-39114200	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr2:39104200-39108600	Weak transcription	Dnd41	blood
12	chr2:39104200-39109000	Weak transcription	Stomach Mucosa	stomach
13	chr2:39104200-39109600	Weak transcription	Adipose Nuclei	Adipose
14	chr2:39104200-39110000	Weak transcription	HMEC	breast
15	chr2:39104200-39110600	Weak transcription	Fetal Stomach	stomach
16	chr2:39104200-39111000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:39104200-39111200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr2:39104200-39111200	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr2:39104200-39111200	Weak transcription	Osteobl	bone
20	chr2:39104200-39111400	Weak transcription	HSMM	muscle
21	chr2:39104200-39111800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:39104200-39111800	Weak transcription	Fetal Kidney	kidney
23	chr2:39104200-39112000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr2:39104200-39112000	Weak transcription	Fetal Muscle Leg	muscle
25	chr2:39104200-39112000	Weak transcription	NHDF-Ad	bronchial
26	chr2:39104200-39112200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr2:39104200-39112400	Weak transcription	Fetal Intestine Small	intestine
28	chr2:39104200-39112600	Weak transcription	Brain Angular Gyrus	brain
29	chr2:39104200-39112800	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr2:39104200-39113400	Weak transcription	Fetal Intestine Large	intestine
31	chr2:39104200-39113400	Weak transcription	Psoas Muscle	Psoas
32	chr2:39104200-39113400	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr2:39104200-39113800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr2:39104200-39113800	Weak transcription	Fetal Lung	lung
35	chr2:39104200-39114400	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr2:39104200-39114400	Weak transcription	Colon Smooth Muscle	Colon
37	chr2:39104200-39114800	Weak transcription	Brain Cingulate Gyrus	brain
38	chr2:39104200-39114800	Weak transcription	Brain Hippocampus Middle	brain
39	chr2:39104200-39115800	Weak transcription	Brain Germinal Matrix	brain
40	chr2:39104200-39119400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr2:39104200-39122200	Weak transcription	Ovary	ovary
42	chr2:39104200-39129000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr2:39107000-39113600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr2:39107400-39108400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr2:39107600-39108400	Strong transcription	Brain Anterior Caudate	brain
46	chr2:39107600-39108400	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr2:39107600-39108600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr2:39107600-39108800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr2:39107600-39108800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr2:39107600-39109000	Strong transcription	Liver	Liver

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